VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 22 2011 - 08:40:16 CDT

Hi Francesco,
I should add/elaborate that while the use of a topology file containing
gaff types is not the source of your current technical problems (which
is what I'm focusing on now), it will be an absolute disaster if you
actually simulate a system mixing gaff ligand types with charmm
protein/lipid types. It will run, but there's no earthly reason why you
should trust the results. You'd be much better off either using amber
protein/lipid as well or switching to the charmm general force field for
your ligand.
Best,
Peter

On 03/22/2011 06:32 AM, Francesco Pietra wrote:
> Hi Peter:
>
> On Tue, Mar 22, 2011 at 1:42 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>> Hi Francesco,
>> Why are you surprised that a *gaff* topology doesn't match *charmm* atom
>> names and types?
>
> I showed that while asking to myself whether autopsf should be able to
> understand such gaff list or a charmm list is a must.
>>
>> Did you try building your molecule with psfgen as I suggested? If you
>> did, and you still have an extra atom, what is it?
>
> I tried, but both psfgen and autopsf drop into "poorly guessed
> coordinates" for most atoms. I came across Jim Phillips' answer to a
> similar problem (insert below). Both psfgen and autopsf do not form
> impropers in psf. Also, psfgen does less than autopsf does, i.e.
> psfgen skips the whole gem-dimethyl portion of ibuprofen. It may be
> too long to examine what happens, however I am showing that below for
> psfgen (for autopsf is much longer). I wonder whether there is a
> here-missing statement for psfgen to indicate that topology comes from
> GAFF. As I said, I hope one day to deal with organic molecules through
> paratool, once the promised gamess-us support is activated.
>
> *****************
> IBUPROFEN:
> ATOM 1 C RIB 1 0.024 1.891 0.260 1.00 0.00
> ATOM 2 C RIB 1 -0.888 1.078 0.950 1.00 0.00
> ATOM 3 C RIB 1 -0.937 -0.300 0.713 1.00 0.00
> ATOM 4 C RIB 1 -0.075 -0.891 -0.221 1.00 0.00
> ATOM 5 C RIB 1 0.832 -0.079 -0.916 1.00 0.00
> ATOM 6 C RIB 1 0.880 1.299 -0.679 1.00 0.00
> ATOM 7 C RIB 1 -0.119 -2.378 -0.480 1.00 0.00
> ATOM 8 C RIB 1 1.062 -3.125 0.170 1.00 0.00
> ATOM 9 C RIB 1 1.070 -2.951 1.698 1.00 0.00
> ATOM 10 C RIB 1 1.013 -4.619 -0.193 1.00 0.00
> ATOM 11 C RIB 1 0.062 3.375 0.526 1.00 0.00
> ATOM 12 C RIB 1 -0.993 4.116 -0.266 1.00 0.00
> ATOM 13 O RIB 1 -1.816 4.884 0.169 1.00 0.00
> ATOM 14 O RIB 1 -0.941 3.796 -1.561 1.00 0.00
> ATOM 15 H RIB 1 -1.603 4.214 -2.135 1.00 0.00
> ATOM 16 C RIB 1 1.433 3.991 0.259 1.00 0.00
> ATOM 17 H RIB 1 -1.572 1.527 1.685 1.00 0.00
> ATOM 18 H RIB 1 -1.657 -0.922 1.264 1.00 0.00
> ATOM 19 H RIB 1 1.513 -0.527 -1.654 1.00 0.00
> ATOM 20 H RIB 1 1.596 1.922 -1.235 1.00 0.00
> ATOM 21 H RIB 1 -0.132 -2.559 -1.575 1.00 0.00
> ATOM 22 H RIB 1 -1.082 -2.786 -0.109 1.00 0.00
> ATOM 23 H RIB 1 1.993 -2.688 -0.222 1.00 0.00
> ATOM 24 H RIB 1 0.144 -3.380 2.134 1.00 0.00
> ATOM 25 H RIB 1 1.948 -3.470 2.135 1.00 0.00
> ATOM 26 H RIB 1 1.124 -1.873 1.957 1.00 0.00
> ATOM 27 H RIB 1 0.079 -5.073 0.197 1.00 0.00
> ATOM 28 H RIB 1 1.042 -4.743 -1.295 1.00 0.00
> ATOM 29 H RIB 1 1.883 -5.146 0.251 1.00 0.00
> ATOM 30 H RIB 1 -0.163 3.478 1.598 1.00 0.00
> ATOM 31 H RIB 1 1.687 3.902 -0.818 1.00 0.00
> ATOM 32 H RIB 1 2.208 3.467 0.856 1.00 0.00
> ATOM 33 H RIB 1 1.428 5.065 0.540 1.00 0.00
> CONECT 1 2 2 6 11
> CONECT 2 1 1 3 17
> CONECT 3 2 4 4 18
> CONECT 4 3 3 5 7
> CONECT 5 4 6 6 19
> CONECT 6 1 5 5 20
> CONECT 7 4 8 21 22
> CONECT 8 7 9 10 23
> CONECT 9 8 24 25 26
> CONECT 10 8 27 28 29
> CONECT 11 1 12 16 30
> CONECT 12 11 13 13 14
> CONECT 13 12 12
> CONECT 14 12 15
> CONECT 15 14
> CONECT 16 11 31 32 33
> CONECT 17 2
> CONECT 18 3
> CONECT 19 5
> CONECT 20 6
> CONECT 21 7
> CONECT 22 7
> CONECT 23 8
> CONECT 24 9
> CONECT 25 9
> CONECT 26 9
> CONECT 27 10
> CONECT 28 10
> CONECT 29 10
> CONECT 30 11
> CONECT 31 16
> CONECT 32 16
> CONECT 33 16
> MASTER 0 0 0 0 0 0 0 0 33 0 33 0
> END
> *****************
> * Topology File obtained with CHARMMGEN.
> *
> 99 1
> MASS 1 c3 12.010000
> MASS 2 os 16.000000
> MASS 3 oh 16.000000
> MASS 4 ho 1.008000
> MASS 5 hc 1.008000
>
> RESI RIB -0.000
> GROUP
> ATOM C c3 -0.090500
> ATOM C1 c3 -0.073000
> ATOM C2 c3 -0.090900
> ATOM C3 c3 -0.057900
> ATOM C4 c3 -0.090600
> ATOM C5 c3 -0.072700
> ATOM C6 c3 -0.045300
> ATOM C7 c3 -0.063900
> ATOM C8 c3 -0.091700
> ATOM C9 c3 -0.091800
> ATOM C10 c3 -0.010400
> ATOM C11 c3 0.525500
> ATOM O os -0.502400
> ATOM O1 oh -0.590400
> ATOM H ho 0.443300
> ATOM C12 c3 -0.089600
> ATOM H1 hc 0.094200
> ATOM H2 hc 0.095100
> ATOM H3 hc 0.095400
> ATOM H4 hc 0.108900
> ATOM H5 hc 0.051300
> ATOM H6 hc 0.049500
> ATOM H7 hc 0.050600
> ATOM H8 hc 0.032200
> ATOM H9 hc 0.034500
> ATOM H10 hc 0.040300
> ATOM H11 hc 0.034300
> ATOM H12 hc 0.032900
> ATOM H13 hc 0.036300
> ATOM H14 hc 0.086100
> ATOM H15 hc 0.056900
> ATOM H16 hc 0.050400
> ATOM H17 hc 0.043200
>
> BOND C C1 ! dist 1.4031
> BOND C C5 ! dist 1.4018
> BOND C C10 ! dist 1.5081
> BOND C1 C2 ! dist 1.3991
> BOND C1 H1 ! dist 1.0999
> BOND C2 C3 ! dist 1.4017
> BOND C2 H2 ! dist 1.0995
> BOND C3 C4 ! dist 1.4018
> BOND C3 C6 ! dist 1.5100
> BOND C4 C5 ! dist 1.3991
> BOND C4 H3 ! dist 1.0996
> BOND C5 H4 ! dist 1.1000
> BOND C6 C7 ! dist 1.5412
> BOND C6 H5 ! dist 1.1099
> BOND C6 H6 ! dist 1.1097
> BOND C7 C8 ! dist 1.5379
> BOND C7 C9 ! dist 1.5382
> BOND C7 H7 ! dist 1.1006
> BOND C8 H8 ! dist 1.1098
> BOND C8 H9 ! dist 1.1096
> BOND C8 H10 ! dist 1.1100
> BOND C9 H11 ! dist 1.1093
> BOND C9 H12 ! dist 1.1093
> BOND C9 H13 ! dist 1.1098
> BOND C10 C11 ! dist 1.5131
> BOND C10 C12 ! dist 1.5266
> BOND C10 H14 ! dist 1.1002
> BOND C11 O ! dist 1.2068
> BOND C11 O1 ! dist 1.3350
> BOND O1 H ! dist 0.9708
> BOND C12 H15 ! dist 1.1101
> BOND C12 H16 ! dist 1.1098
> BOND C12 H17 ! dist 1.1102
>
> ANGL C C1 C2 ! angle 120.6733
> ANGL C C1 H1 ! angle 119.7556
> ANGL C C5 C4 ! angle 120.5638
> ANGL C C5 H4 ! angle 119.7952
> ANGL C C10 C11 ! angle 111.8394
> ANGL C C10 C12 ! angle 112.8827
> ANGL C C10 H14 ! angle 105.0005
> ANGL C1 C C5 ! angle 118.7914
> ANGL C1 C C10 ! angle 119.9858
> ANGL C1 C2 C3 ! angle 120.4391
> ANGL C1 C2 H2 ! angle 119.6850
> ANGL C2 C1 H1 ! angle 119.5711
> ANGL C2 C3 C4 ! angle 118.9498
> ANGL C2 C3 C6 ! angle 120.7692
> ANGL C3 C2 H2 ! angle 119.8759
> ANGL C3 C4 C5 ! angle 120.5808
> ANGL C3 C4 H3 ! angle 119.8327
> ANGL C3 C6 C7 ! angle 112.4967
> ANGL C3 C6 H5 ! angle 109.2772
> ANGL C3 C6 H6 ! angle 109.2686
> ANGL C4 C3 C6 ! angle 120.2809
> ANGL C4 C5 H4 ! angle 119.6410
> ANGL C5 C C10 ! angle 121.2206
> ANGL C5 C4 H3 ! angle 119.5865
> ANGL C6 C7 C8 ! angle 111.6038
> ANGL C6 C7 C9 ! angle 110.2924
> ANGL C6 C7 H7 ! angle 107.7903
> ANGL C7 C6 H5 ! angle 110.2436
> ANGL C7 C6 H6 ! angle 110.2292
> ANGL C7 C8 H8 ! angle 110.0150
> ANGL C7 C8 H9 ! angle 110.0291
> ANGL C7 C8 H10 ! angle 109.9968
> ANGL C7 C9 H11 ! angle 109.9589
> ANGL C7 C9 H12 ! angle 110.0081
> ANGL C7 C9 H13 ! angle 109.9868
> ANGL C8 C7 C9 ! angle 110.1523
> ANGL C8 C7 H7 ! angle 107.7308
> ANGL C9 C7 H7 ! angle 109.1790
> ANGL C10 C11 O ! angle 126.7620
> ANGL C10 C11 O1 ! angle 111.2980
> ANGL C10 C12 H15 ! angle 110.0489
> ANGL C10 C12 H16 ! angle 110.0328
> ANGL C10 C12 H17 ! angle 110.0025
> ANGL C11 C10 C12 ! angle 109.6965
> ANGL C11 C10 H14 ! angle 108.7587
> ANGL C11 O1 H ! angle 116.3462
> ANGL O C11 O1 ! angle 121.9228
> ANGL C12 C10 H14 ! angle 108.4401
> ANGL H5 C6 H6 ! angle 105.0523
> ANGL H8 C8 H9 ! angle 108.9476
> ANGL H8 C8 H10 ! angle 108.9258
> ANGL H9 C8 H10 ! angle 108.8968
> ANGL H11 C9 H12 ! angle 108.9964
> ANGL H11 C9 H13 ! angle 108.9672
> ANGL H12 C9 H13 ! angle 108.8953
> ANGL H15 C12 H16 ! angle 108.9207
> ANGL H15 C12 H17 ! angle 108.9144
> ANGL H16 C12 H17 ! angle 108.8910
>
> DIHE C5 C C1 C2 ! dihe 0.4381
> DIHE C10 C C1 C2 ! dihe 179.9017
> DIHE C5 C C1 H1 ! dihe -179.5632
> DIHE C10 C C1 H1 ! dihe -0.0996
> DIHE C1 C C5 C4 ! dihe -0.4699
> DIHE C10 C C5 C4 ! dihe -179.9267
> DIHE C1 C C5 H4 ! dihe 179.5264
> DIHE C10 C C5 H4 ! dihe 0.0696
> DIHE C1 C C10 C11 ! dihe -83.0016
> DIHE C5 C C10 C11 ! dihe 96.4488
> DIHE C1 C C10 C12 ! dihe 152.7168
> DIHE C5 C C10 C12 ! dihe -27.8329
> DIHE C1 C C10 H14 ! dihe 34.7772
> DIHE C5 C C10 H14 ! dihe -145.7725
> DIHE C C1 C2 C3 ! dihe -0.0888
> DIHE H1 C1 C2 C3 ! dihe 179.9125
> DIHE C C1 C2 H2 ! dihe 179.9054
> DIHE H1 C1 C2 H2 ! dihe -0.0933
> DIHE C1 C2 C3 C4 ! dihe -0.2322
> DIHE H2 C2 C3 C4 ! dihe 179.7735
> DIHE C1 C2 C3 C6 ! dihe 179.8375
> DIHE H2 C2 C3 C6 ! dihe -0.1567
> DIHE C2 C3 C4 C5 ! dihe 0.2002
> DIHE C6 C3 C4 C5 ! dihe -179.8692
> DIHE C2 C3 C4 H3 ! dihe -179.8311
> DIHE C6 C3 C4 H3 ! dihe 0.0996
> DIHE C2 C3 C6 C7 ! dihe -104.5055
> DIHE C4 C3 C6 C7 ! dihe 75.5651
> DIHE C2 C3 C6 H5 ! dihe 132.7015
> DIHE C4 C3 C6 H5 ! dihe -47.2278
> DIHE C2 C3 C6 H6 ! dihe 18.2628
> DIHE C4 C3 C6 H6 ! dihe -161.6665
> DIHE C3 C4 C5 C ! dihe 0.1538
> DIHE H3 C4 C5 C ! dihe -179.8150
> DIHE C3 C4 C5 H4 ! dihe -179.8425
> DIHE H3 C4 C5 H4 ! dihe 0.1887
> DIHE C3 C6 C7 C8 ! dihe 60.5098
> DIHE H5 C6 C7 C8 ! dihe -177.2417
> DIHE H6 C6 C7 C8 ! dihe -61.7171
> DIHE C3 C6 C7 C9 ! dihe -176.7048
> DIHE H5 C6 C7 C9 ! dihe -54.4563
> DIHE H6 C6 C7 C9 ! dihe 61.0683
> DIHE C3 C6 C7 H7 ! dihe -57.5941
> DIHE H5 C6 C7 H7 ! dihe 64.6543
> DIHE H6 C6 C7 H7 ! dihe -179.8211
> DIHE C6 C7 C8 H8 ! dihe 61.8348
> DIHE C9 C7 C8 H8 ! dihe -61.0307
> DIHE H7 C7 C8 H8 ! dihe 179.9744
> DIHE C6 C7 C8 H9 ! dihe -178.1246
> DIHE C9 C7 C8 H9 ! dihe 59.0099
> DIHE H7 C7 C8 H9 ! dihe -59.9850
> DIHE C6 C7 C8 H10 ! dihe -58.1584
> DIHE C9 C7 C8 H10 ! dihe 178.9761
> DIHE H7 C7 C8 H10 ! dihe 59.9812
> DIHE C6 C7 C9 H11 ! dihe -61.7756
> DIHE C8 C7 C9 H11 ! dihe 61.8555
> DIHE H7 C7 C9 H11 ! dihe 179.9622
> DIHE C6 C7 C9 H12 ! dihe 58.2767
> DIHE C8 C7 C9 H12 ! dihe -178.0921
> DIHE H7 C7 C9 H12 ! dihe -59.9855
> DIHE C6 C7 C9 H13 ! dihe 178.2216
> DIHE C8 C7 C9 H13 ! dihe -58.1472
> DIHE H7 C7 C9 H13 ! dihe 59.9595
> DIHE C C10 C11 O ! dihe 127.2348
> DIHE C12 C10 C11 O ! dihe -106.7208
> DIHE H14 C10 C11 O ! dihe 11.7296
> DIHE C C10 C11 O1 ! dihe -51.2682
> DIHE C12 C10 C11 O1 ! dihe 74.7762
> DIHE H14 C10 C11 O1 ! dihe -166.7734
> DIHE C C10 C12 H15 ! dihe 64.1365
> DIHE C11 C10 C12 H15 ! dihe -61.3117
> DIHE H14 C10 C12 H15 ! dihe -179.9591
> DIHE C C10 C12 H16 ! dihe -55.8945
> DIHE C11 C10 C12 H16 ! dihe 178.6573
> DIHE H14 C10 C12 H16 ! dihe 60.0099
> DIHE C C10 C12 H17 ! dihe -175.8594
> DIHE C11 C10 C12 H17 ! dihe 58.6924
> DIHE H14 C10 C12 H17 ! dihe -59.9550
> DIHE C10 C11 O1 H ! dihe 178.4926
> DIHE O C11 O1 H ! dihe -0.0944
> ***************
>
> PSFGEN TERMINAL OUTPUT
>
> francesco_at_tya64:~/RIBr_ac_psfgen$ psfgen << ENDMOL
>> topology RIB.rtf
>> segment RI {
>> pdb RIB.pdb
>> }
>>
>> coordpdb RIB.pdb RI
>>
>> guesscoord
>>
>> writepsf rib.psf
>> writepdb rib.pdb
>>
>> ENDMOL
> PSFGEN 1.5.0 from NAMD CVS-2011-02-14 for Linux-x86_64
> reading topology file RIB.rtf
>
> Topology File.
>
> Created by CHARMM version 99 1
> building segment RI
> reading residues from pdb file RIB.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> reading coordinates from pdb file RIB.pdb for segment RI
> Info: guessing coordinates for 30 atoms (13 non-hydrogen)
> Warning: poorly guessed coordinates for 16 atoms (10 non-hydrogen):
> Warning: poorly guessed coordinate for atom C1 RIB:1 RI
> Warning: poorly guessed coordinate for atom C2 RIB:1 RI
> Warning: poorly guessed coordinate for atom C3 RIB:1 RI
> Warning: poorly guessed coordinate for atom C4 RIB:1 RI
> Warning: poorly guessed coordinate for atom C5 RIB:1 RI
> Warning: poorly guessed coordinate for atom C6 RIB:1 RI
> Warning: poorly guessed coordinate for atom C7 RIB:1 RI
> Warning: poorly guessed coordinate for atom C10 RIB:1 RI
> Warning: poorly guessed coordinate for atom C11 RIB:1 RI
> Warning: poorly guessed coordinate for atom O1 RIB:1 RI
> Warning: poorly guessed coordinate for atom H1 RIB:1 RI
> Warning: poorly guessed coordinate for atom H2 RIB:1 RI
> Warning: poorly guessed coordinate for atom H3 RIB:1 RI
> Warning: poorly guessed coordinate for atom H4 RIB:1 RI
> Warning: poorly guessed coordinate for atom H5 RIB:1 RI
> Warning: poorly guessed coordinate for atom H6 RIB:1 RI
> Warning: failed to guess coordinates for 14 atoms
>
> MY INSERT: For hemoglobin similar warning, Jim Phillips answered Fri
> Aug 2010: Those "poorly guessed coordinates" warnings are not unusual.
> It just means psfgen had to use an internal heuristic rather than the
> pdb file or a rule in the topology file to assign positions to those
> atoms. If the system looks normal, minimizes, and runs you're probably
> fine. If not, those atoms are a good place to look ".
>
>
> Info: writing psf file rib.psf
> total of 33 atoms
> total of 33 bonds
> total of 58 angles
> total of 80 dihedrals
> total of 0 impropers
> total of 0 cross-terms
> Info: psf file complete.
> Info: writing pdb file rib.pdb
> Info: Atoms with guessed coordinates will have occupancy of 0.0.
> Info: pdb file complete.
> francesco_at_tya64:~/RIBr_ac_psfgen$
> ******************************
>
> TERMINAL OUTPUT FROM VMD FOR THESE .psf/.pdb
> vmd > Info) Using plugin psf for structure file
> /home/francesco/RIBr_ac_psfgen/rib.psf
> psfplugin) WARNING: no impropers defined in PSF file.
> psfplugin) no cross-terms defined in PSF file.
> Info) Analyzing structure ...
> Info) Atoms: 33
> Info) Bonds: 33
> Info) Angles: 58 Dihedrals: 80 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 0 Nucleic: 0
> Info) Using plugin pdb for coordinates from file
> /home/francesco/RIBr_ac_psfgen/rib.pdb
> Info) Finished with coordinate file /home/francesco/RIBr_ac_psfgen/rib.pdb.
>
> Thanks
> francesco
> **********************************
> **********************************
>
>
>>
>> Peter
>>
>> On 03/21/2011 12:50 PM, Francesco Pietra wrote:
>>> Hi Peter:
>>> I have checked all bonds, angles, and dihedrals in the .rtf topology
>>> file created with antechamber-charmmgen. They are correct. However,
>>> the .rtf list below has no correspondence in top_all27_ prot_lipid.rtf
>>> (which I used for the protein and the lipidic membrane) and seem to be
>>> related to the lower-case usage - without dots - in GAFF ff of
>>> antechamber. Could that be at the origin of the mess?
>>>
>>> *********************************
>>> * Topology File.
>>> *
>>> 99 1
>>> MASS 1 ca 12.010000
>>> MASS 2 c3 12.010000
>>> MASS 3 ha 1.008000
>>> MASS 4 hc 1.008000
>>> MASS 5 c 12.010000
>>> MASS 6 o 16.000000
>>> MASS 7 oh 16.000000
>>> MASS 8 ho 1.008000
>>>
>>> RESI RIB 0.002
>>> GROUP
>>> ATOM C ca -0.097300
>>> ATOM C1 ca -0.112000
>>> ATOM C2 ca -0.130000
>>> ATOM C3 ca -0.065300
>>> ATOM C4 ca -0.130000
>>> ATOM C5 ca -0.112000
>>> ATOM C6 c3 -0.038100
>>> ATOM C7 c3 -0.063700
>>> ATOM C8 c3 -0.092100
>>> ATOM C9 c3 -0.092100
>>> ATOM C10 c3 -0.053400
>>> ATOM H ha 0.134000
>>> ATOM H4 ha 0.135000
>>> ATOM H5 ha 0.135000
>>> ATOM H6 ha 0.148000
>>> ATOM H7 hc 0.049700
>>> ATOM H8 hc 0.050700
>>> ATOM H9 hc 0.031700
>>> ATOM H10 hc 0.039700
>>> ATOM H11 hc 0.034700
>>> ATOM H12 hc 0.032700
>>> ATOM H13 hc 0.034700
>>> ATOM H14 hc 0.036700
>>> ATOM H15 hc 0.051700
>>> ATOM C11 c 0.639100
>>> ATOM O o -0.548000
>>> ATOM O1 oh -0.608100
>>> ATOM H16 ho 0.443000
>>> ATOM C12 c3 -0.089100
>>> ATOM H17 hc 0.085700
>>> ATOM H1 hc 0.043700
>>> ATOM H2 hc 0.050700
>>> ATOM H3 hc 0.056700
>>>
>>>
>>> here
>>>
>>> ca: aromatic C
>>>
>>> c3: ali C
>>>
>>> ha: H at aromatic C
>>>
>>> hc: H at ali C
>>>
>>> c: carbonyl C
>>>
>>> o: carbonyl O
>>>
>>> oh: oxygen of -OH
>>>
>>> ho: H of -OH
>>> ******************************
>>>
>>> Thanks a lot for opinions about
>>>
>>> francesco
>>>
>>> On Mon, Mar 21, 2011 at 11:48 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>>>> Hi Francesco,
>>>> The key question is, are the CHARMMGEN .inp/.rtf files correct? Either
>>>> they are wrong, or one of the assumptions that autopsf makes is invalid
>>>> for that structure and you need to change your settings. The best way to
>>>> check is to (a) manually inspect the .inp/.rtf files and make sure that
>>>> the atoms and connectivity match your expectations, and (b) try
>>>> generating the ibuprofen using psfgen instead of autopsf so that you
>>>> have finer control over what is being done to the molecule.
>>>>
>>>> Best,
>>>> Peter
>>>>
>>>> On 03/21/2011 06:12 AM, Francesco Pietra wrote:
>>>>> Hi:
>>>>> I wonder whether there is experience with coming to AUTOPSF with
>>>>> .inp/.rtf files generated for non-protein organic molecules with the
>>>>> AMBER10's tool CHARMMGEN. The web is silent to this concern.
>>>>>
>>>>> I am in trouble with ANTECHAMBER-CHARMMGEN for complex non-proteic
>>>>> ligands. Thererore, I tried with a simple ligand, ibuprofen. Using .ac
>>>>> type files (not .mol2 which caused immediately troubles to CHARMMGEN)
>>>>> from ANTECHAMBER, CHARMMGEN generated .inp/.rtf files that were
>>>>> accepted as topology by AUTOPSF, getting .psf/.pdb. AUTOPSF counted 34
>>>>> atoms, which I corrected to 33, as they are. However, loading these
>>>>> files to VMD, bond connections appear heavily altered. No more
>>>>> ibuprofen.
>>>>>
>>>>> Uncertain whether problems arising from my skipping PARATOOL (I am no
>>>>> GAUSSIAN owner) can be posted here, to avoid overloading the mailing
>>>>> list, I am not attaching files here. However, I would be happy to do
>>>>> that if there is interest (or kindness to help)
>>>>>
>>>>> Thanks
>>>>>
>>>>> francesco pietra
>>>>
>>