VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Dec 05 2009 - 12:51:22 CST
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Hi Peter:
I repeated the solvation procedure to check for input errors, setting,
as before:
--Use Mol Dimensions
Box Padding 15 throughout
--Use non standard solvent
--Sol box pdb: cgwat.pdb
--Sol box psf: cgwat.psf
--Sol box top: rbcg-2007.top
Sol box side l: 40
Sol box key sel: name cgw
This time the log:
generating solute plus one replica of water...
generating water residue lists...
single water residue type, creating residue list...
replicating 64 water segments, 4 by 4 by
Therefore, I must assume that in previous trials I did some errors.
However, the screen output ends with:
nfo) Analyzing structure ...
Info) Atoms: 41282
Info) Bonds: 3845
Info) Angles: 5028 Dihedrals: 6136 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 38704
Info) Waters: 37308
Info) Segments: 102
Info) Fragments: 37437 Protein: 0 Nucleic: 0
Info) Using plugin pdb for coordinates from file solvate.pdb
Info) Finished with coordinate file solvate.pdb.
Info) Opened coordinate file solvate.pdb for writing.
Info) Extra structure overlap safety check...
-error Found 2273 water atoms near the solute! Please report this bug to
-error vmd_at_ks.uiuc.edu
Again, the box is cubic and the protein+membrane is not well centered.
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, Dec 5, 2009 at 5:07 PM
Subject: Re: vmd-l: Failure with AutoPSF (PDB has x, y, z zero)
To: Peter Freddolino <petefred_at_ks.uiuc.edu>
Hi Peter:
Sorry for bothering the users with my mistakes. I had forgot to
replace with rbcg-2007.top the topology that comes automatically when
AutoPSF is opened. Now it works.
Solvation with AddSolvationBox cgwat did npot proceed as expected. I
got .psf .pdb files that open correctly, but errors were signaled
during the execution. Saved to log:
Running solvate with arguments:
cg_combined.popc+mod21.edited_autopsf.psf
cg_combined.popc+mod21.edited_autopsf.pdb -o solvate -s WT -x 15 -y 15
-z 15 +x 15 +y 15 +z 15 -b 2.4 -spdb cgwat.pdb -spsf cgwat.psf -stop
rbcg-2007.top -ws 40 -ks {name cgw}
generating solute plus one replica of water...
generating water residue lists...
single water residue type, creating residue list...
replicating 64 water segments, 4 by 4 by 4
error $errMsg $savedInfo $savedCode }"
(procedure "solvate" line 8)
invoked from within
"solvate {cg_combined.popc+mod21.edited_autopsf.psf}
{cg_combined.popc+mod21.edited_autopsf.pdb} -o solvate -s WT -x 15 -y
15 -z 15 +x 15 +y 15 +z 15 -..."
("eval" body line 1)
invoked from within
"eval solvate $command_line"
(procedure "::Solvate::run_solvate" line 96)
invoked from within
"::Solvate::run_solvate"
invoked from within
".solvategui.solvate invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .solvategui.solvate"
(command bound to event)
The box is cubic and too big for a Box Padding of 15 A. Also, the
protein+membrane is not centered in the water box. When I solvated the
protein alone with same settings
--Use mol dimensions
-- Box Padding 15
--topol rbcg-2007.top
--Side length 40
--key sel "name cgw"
the box was well shaped around the elongated protein. The protein +
membrane is elongated the same fashion.
Incidentally, does Autosolvationbox take into account clashes?
thanks
francesco
thanks
francesco
On Sat, Dec 5, 2009 at 3:21 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Francesco,
> did you use a CG topology file? It looks like you tried to use an all
> atom topology file with your CG protein, which is not going to work...
> Best,
> Peter
>
> Francesco Pietra wrote:
>> Hi:
>> I wonder whether by simply showing sections of an input
>> cg-protein-bilayer.pdb may suggest why the resulting pdb has zero
>> value for all coordinates, while the psf was formed. I used VMD 1.8.7
>> with the Nov 5, 2009 version of autopsf.tcl (sourced before using
>> AutoPSF, and used successfully with the cg-protein.pdb alone).
>>
>> Start of file:
>>
>> ATOM 1 BB LEU A 1 94.117 6.647 33.003 1.00 0.00 C
>> ATOM 2 LEU2 LEU A 1 91.702 4.673 31.893 1.00 0.00 C
>> ATOM 3 BB SER A 2 96.602 4.840 33.767 1.00 0.00 C
>>
>> ......................
>>
>>
>> End 1st subunit and start of 2nd (similarly for the other subunits):
>>
>> ATOM 834 LYS2 LYS A 426 87.486 15.560 52.901 1.00 0.00 C
>> ATOM 836 BB LEU B 1 63.700 14.066 32.470 1.00 0.00 C
>> ATOM 837 LEU2 LEU B 1 62.820 11.464 34.800 1.00 0.00 C
>> ATOM 838 BB SER B 2 66.653 14.844 33.474 1.00 0.00 C
>> ATOM 839 SER2 SER B 2 66.910 16.287 35.447 1.00 0.00 C
>>
>> .........................
>>
>> End of protein and start of lipid:
>>
>> ATOM 2484 ALA2 ALA C 419 100.557 15.272 22.450 1.00 0.00 C
>> ATOM 2485 BB TYR C 420 99.103 10.800 24.846 1.00 0.00 C
>> ATOM 2486 TYR2 TYR C 420 101.793 14.152 26.627 1.00 0.00 C
>> ATOM 1 CHO POPCL 1 45.698 63.146 8.734 1.00 0.00 N
>> ATOM 2 PHO POPCL 1 48.402 64.504 6.458 1.00 0.00 P
>> ATOM 3 ES1 POPCL 1 49.993 59.387 4.107 1.00 0.00 C
>>
>> It may be noticed that the lipid atom name is placed at 13,14,15 while
>> in cg.membrane obtained with VMD is at 14,15,16. Actually, I combined
>> protein and membrane (and removed clashes) outside VMD (in the past I
>> was unable to do so with VMD).
>> ..................................
>>
>> "Interface" lipid-water:
>>
>> ATOM 2728 ME6 POPCL 19 109.251 34.896 60.703 1.00 0.00 C
>> ATOM 2729 MT2 POPCL 19 107.211 38.181 61.495 1.00 0.00 C
>> ATOM 2730 H2O TIP3W 2 132.301 54.580 49.722 1.00 0.00 O
>> ATOM 2731 H2O TIP3W 22 130.101 22.103 32.812 1.00 0.00 O
>> ATOM 2732 H2O TIP3W 35 109.445 25.664 35.058 1.00 0.00 O
>>
>> .....................
>>
>> End of file:
>>
>> ATOM 3043 H2O TIP3W4585 112.752 66.685 58.218 1.00 0.00 O
>> ATOM 3044 H2O TIP3W4966 109.811 68.176 58.019 1.00 0.00 O
>> END
>> =================
>>
>> The output pdb:
>>
>> ATOM 1 N LEU A 1 0.000 0.000 0.000 -1.00 0.00 P1 N
>> ATOM 2 HN LEU A 1 0.000 0.000 0.000 -1.00 0.00 P1 H
>> ATOM 3 CA LEU A 1 0.000 0.000 0.000 -1.00 0.00 P1 C
>>
>> The output psf:
>>
>> PSF CMAP
>>
>> 40 !NTITLE
>> REMARKS original generated structure x-plor psf file
>> REMARKS topology popc+mod21_autopsf-temp.top
>> REMARKS segment P1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment P2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment P3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O4 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O5 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O6 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O7 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O8 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W1 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O9 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O10 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O11 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O12 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O13 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O14 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O15 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O16 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O17 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O18 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W2 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O19 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O20 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O21 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O22 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O23 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O24 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W3 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O25 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O26 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O27 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O28 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O29 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O30 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment O31 { first NONE; last NONE; auto angles dihedrals }
>> REMARKS segment W4 { first NONE; last NONE; auto angles dihedrals }
>>
>> 41610 !NATOM
>> 1 P1 1 LEU N NH1 -0.470000 14.0070 0
>> 2 P1 1 LEU HN H 0.310000 1.0080 0
>> 3 P1 1 LEU CA CT1 0.070000 12.0110 0
>> 4 P1 1 LEU HA HB 0.090000 1.0080 0
>> 5 P1 1 LEU CB CT2 -0.180000 12.0110 0
>> 6 P1 1 LEU HB1 HA 0.090000 1.0080 0
>> 7 P1 1 LEU HB2 HA 0.090000 1.0080 0
>> 8 P1 1 LEU CG CT1 -0.090000 12.0110 0
>> 9 P1 1 LEU HG HA 0.090000 1.0080 0
>> .........................
>> ..................
>> ===============
>>
>> Of course, this psf does not match with the input pdb.
>> =========
>>
>> thanks
>> francesco pietra
>>
>
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