VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Mar 27 2015 - 06:11:27 CDT

1) you are modifying the end terminals of the protein which is usually done
or not done depending on the case at hand.

2) the three more atoms have not been added to the copper, the are
incorrect capping of your C-terminal ... Use the appropriate patch to fix
the c-terminal of your protein.

3) if you succeeded in creating the PSF file with the copper in there and
the copper shows in the PSF/pdb -- then you just need to use the cter patch
correctly to solve this issue of yours.
On Mar 28, 2015 12:04 AM, "zoran" <zmatovic_at_kg.ac.rs> wrote:

>
>
> Well I did it with both approach (psfgen and autopsf using GUI) but the
> same error appeared. Meanwhile, I succeded to create psf and pdb files but
> psfgen added three more atoms to CU1 ionic residue (without coordinates). I
> wonder how to eliminate these atoms (i.e. how to change pdb and psf
> removing these excess of atoms?)? I used top_all27_prot_na.rtf topology
> file with additional Cu type and resi CU1
>
> MASS 200 CU 63.55 CU! copper ion
> .....................
> RESI CU1 1.0! note: this atx1 copper
> GROUP ! charmm charge
> ATOM CU Cu 0.15000
> PATCHING FIRST NONE LAST NONE
>
> end of pdb file:
>
>
> ATOM 1180 C LEU A 73 -4.703 -11.142 -8.302 1.00 0.00
> L C
> ATOM 1181 O LEU A 73 -4.144 -11.157 -7.174 1.00 0.00
> L O
> ATOM 1182 C CU1 A 74 0.000 0.000 0.000 -1.00 0.00
> L C
> ATOM 1183 OT1 CU1 A 74 0.000 0.000 0.000 -1.00 0.00
> L O
> ATOM 1184 OT2 CU1 A 74 0.000 0.000 0.000 -1.00 0.00
> L O
> ATOM 1185 CU CU1 A 74 1.320 12.645 0.576 1.00 0.00
> L CU
> END
>
> The yellow atoms are psfgen added and not nedeed
>
> regards
>
> Zoran
>
>
>
>
>
>
>
> Did you pass an appropriate topology to the psfgen plugin. I would suggest
> taking it through the graphical user interface (automatic psf builder) and
> try reproducing the error.
> On Mar 27, 2015 8:10 AM, "zoran" <zmatovic_at_kg.ac.rs> wrote:
>
>>
>> Hello,
>> I think I have might be similar problem. I have to create pdb and psf
>> files of a metallo chaperon (code 1fd8). The problem is that neither
>> autospf nor spfgen want create psf files. I followed procedure written in
>> namd tutorial but nothing. I just succeeded to wrote files for protein but
>> not for whole molecule including metal (Cu). psfgen usually reports an
>> error (with an option by selecting “all”) concerning CTERM end of the
>> protein (LEU 73) that means it found missing N and O atoms (whats not
>> possible – atoms are written in the pdb file). When selected just protein
>> the psfgen behave normally.
>>
>> I entered Cu type and CU1 residue into top file:
>>
>> RESIDUE CU1 -1.0 ! note: this atx1 copper
>> GROUP ! parameterized charge
>> ATOM CU Cu 0.15000
>>
>> END
>>
>> This is the start and the end of my pdb file:
>>
>> START
>> .......................
>> REMARK 900 METALLOCHAPERONE PROTEIN AT 1.02 A
>> RESOLUTION
>> DBREF 1FD8 A 1 73 UNP P38636 ATX1_YEAST 1
>> 73
>> SEQRES 1 A 73 MET ALA GLU ILE LYS HIS TYR GLN PHE ASN VAL VAL
>> MET
>> SEQRES 2 A 73 THR CYS SER GLY CYS SER GLY ALA VAL ASN LYS VAL
>> LEU
>> SEQRES 3 A 73 THR LYS LEU GLU PRO ASP VAL SER LYS ILE ASP ILE
>> SER
>> SEQRES 4 A 73 LEU GLU LYS GLN LEU VAL ASP VAL TYR THR THR LEU
>> PRO
>> SEQRES 5 A 73 TYR ASP PHE ILE LEU GLU LYS ILE LYS LYS THR GLY
>> LYS
>> SEQRES 6 A 73 GLU VAL ARG SER GLY LYS GLN
>> LEU
>> HET CU1 A 74
>> 1
>> HETNAM CU1 COPPER (I)
>> ION
>> FORMUL 2 CU1 CU
>> 1+
>> HELIX 1 1 GLY A 17 GLU A 30 1
>> 14
>> HELIX 2 2 PRO A 52 THR A 63 1
>> 12
>> SHEET 1 A 4 LYS A 35 SER A 39
>> 0
>> SHEET 2 A 4 LEU A 44 THR A 49 -1 O LEU A 44 N SER A
>> 39
>> SHEET 3 A 4 LYS A 5 VAL A 11 -1 N LYS A 5 O THR A
>> 49
>> SHEET 4 A 4 VAL A 67 LEU A 73 -1 N ARG A 68 O ASN A
>> 10
>> LINK CU CU1 A 74 SG CYS A 18 1555 1555
>> 2.12
>> LINK CU CU1 A 74 SG CYS A 15 1555 1555
>> 2.14
>> LINK CU CU1 A 74 N CYS A 15 1555 1555
>> 2.75
>> SITE 1 AC1 4 THR A 14 CYS A 15 CYS A 18 LYS A
>> 65
>> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
>> 1
>> ORIGX1 1.000000 0.000000 0.000000
>> 0.00000
>> ORIGX2 0.000000 1.000000 0.000000
>> 0.00000
>> ORIGX3 0.000000 0.000000 1.000000
>> 0.00000
>> SCALE1 1.000000 0.000000 0.000000
>> 0.00000
>> SCALE2 0.000000 1.000000 0.000000
>> 0.00000
>> SCALE3 0.000000 0.000000 1.000000
>> 0.00000
>> ATOM 1 N MET A 1 -2.865 -21.365 6.547 1.00
>> 0.00 N
>> ATOM 2 CA MET A 1 -2.324 -21.145 5.197 1.00
>> 0.00 C
>> ATOM 3 C MET A 1 -2.826 -19.801 4.702 1.00
>> 0.00 C
>> ATOM 4 O MET A 1 -3.840 -19.328 5.208 1.00
>> 0.00 O
>> ATOM 5 CB MET A 1 -2.806 -22.207 4.194 1.00
>> 0.00 C
>> ATOM 6 CG MET A 1 -2.329 -23.622 4.519 1.00
>> 0.00 C
>> ATOM 7 SD MET A 1 -3.103 -24.357 5.975 1.00
>> 0.00 S
>> .....................................
>> END
>> ...................................
>> ATOM 1160 HE22 GLN 72 -11.615 -9.625 -4.828 0.00
>> 0.00 H
>> ATOM 1161 N LEU 73 -5.839 -9.139 -7.614 0.00
>> 0.00 N
>> ATOM 1162 CA LEU 73 -5.324 -9.822 -8.785 0.00
>> 0.00 C
>> ATOM 1163 C LEU 73 -4.703 -11.142 -8.302 0.00
>> 0.00 C
>> ATOM 1164 OT LEU 73 -4.144 -11.157 -7.174 0.00
>> 0.00 O
>> ATOM 1165 OT1 LEU 73 -4.752 -12.172 -9.009 0.00
>> 0.00 O1-
>> ATOM 1166 CB LEU 73 -4.274 -8.950 -9.489 0.00
>> 0.00 C
>> ATOM 1167 CG LEU 73 -4.872 -7.717 -10.197 0.00
>> 0.00 C
>> ATOM 1168 CD1 LEU 73 -3.786 -6.668 -10.447 0.00
>> 0.00 C
>> ATOM 1169 CD2 LEU 73 -5.498 -8.103 -11.541 0.00
>> 0.00 C
>> ATOM 1170 H LEU 73 -5.263 -9.178 -6.797 0.00
>> 0.00 H
>> ATOM 1171 HA LEU 73 -6.119 -10.017 -9.505 0.00
>> 0.00 H
>> ATOM 1172 HB2 LEU 73 -3.556 -8.606 -8.744 0.00
>> 0.00 H
>> ATOM 1173 HB3 LEU 73 -3.762 -9.560 -10.233 0.00
>> 0.00 H
>> ATOM 1174 HG LEU 73 -5.643 -7.306 -9.545 0.00
>> 0.00 H
>> ATOM 1175 HD11 LEU 73 -3.020 -7.087 -11.100 0.00
>> 0.00 H
>> ATOM 1176 HD12 LEU 73 -3.335 -6.377 -9.498 0.00
>> 0.00 H
>> ATOM 1177 HD13 LEU 73 -4.229 -5.792 -10.922 0.00
>> 0.00 H
>> ATOM 1178 HD21 LEU 73 -4.729 -8.514 -12.196 0.00
>> 0.00 H
>> ATOM 1179 HD22 LEU 73 -5.936 -7.219 -12.006 0.00
>> 0.00 H
>> ATOM 1180 HD23 LEU 73 -6.275 -8.851 -11.379 0.00
>> 0.00 H
>> TER 1181 LEU 73
>> HETATM 1182 CU CU1 74 1.320 12.645 0.576 0.00
>> 0.00 CU2+
>> CONECT 244 1182
>> CONECT 272 1182
>> CONECT 1161 1170 1162
>> CONECT 1162 1171 1166 1163
>> CONECT 1163 1165 1164
>> CONECT 1166 1172 1173 1167
>> CONECT 1167 1174 1168 1169
>> CONECT 1168 1175 1176 1177
>> CONECT 1169 1178 1179 1180
>> END
>>
>> And this is the error that psfgen reports:
>>
>> >Main< (original) 59 % segment L {pdb 1FD8.pdb}
>> psfgen) building segment L
>> psfgen) reading residues from pdb file 1FD8.pdb
>> psfgen) extracted 74 residues from pdb file
>> psfgen) Info: generating structure...psfgen) Info: skipping improper
>> C-CA-N-HN at beginning of segment.
>> psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
>> psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
>> psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue LEU:73
>> psfgen) ERROR: Missing atoms for improper CA(0) N(1) C(0) O(0)
>> in residue LEU:73
>> psfgen) Warning: missing atoms for conformation LEU CA-C-N-CA; skipping.
>> psfgen) Warning: missing atoms for conformation LEU N-CA-C-O; skipping.
>> psfgen) Warning: missing atoms for conformation LEU N-CA-C-N; skipping.
>> psfgen) unknown patch type CTER
>> failed!
>> ERROR: failed on end of segment
>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>
>>
>> Any help is highly welcomed.
>>
>> Zoran
>>
>>
>