[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

[Jignesh Patel]

Dear Justin

I got the solution. I forgot to add residue types in residuetypes.dat

Anyway thanks for your kind reply


with regards,
Jignesh Patel


On Mon, Nov 29, 2010 at 12:17 PM, Jignesh Patel <jbp087 at gmail.com> wrote:

>
> Dear Justin,
>
> Thanks for your reply.
> I have checked whole pdb file. Everything is fine.
>
> When I remove phosphorylated serine and use only serine then every thing
> went fine.
>
> co-ordinates for phosphoserine are as per following
>
> ATOM   1684  N   SEP X 167      27.040  22.580   8.280  1.00
> 0.00
> ATOM   1685  H   SEP X 167      27.150  23.470   7.820  1.00
> 0.00
> ATOM   1686  CA  SEP X 167      28.020  22.270   9.340  1.00
> 0.00
> ATOM   1687  CB  SEP X 167      29.330  21.760   8.740  1.00
> 0.00
> ATOM   1688  OG  SEP X 167      30.210  21.300   9.770  1.00
> 0.00
> ATOM   1689  P   SEP X 167      29.763  21.418  10.657  0.80  0.00
> ATOM   1690  O1P SEP X 167      30.228  20.602  11.000  0.80
> 0.00
> ATOM   1691  O2P SEP X 167      29.298  22.234  10.314  0.80
> 0.00
> ATOM   1692  O3P SEP X 167      29.316  21.536  11.544  0.80  0.00
> ATOM   1693  C   SEP X 167      28.320  23.540  10.140  1.00
> 0.00
> ATOM   1694  O   SEP X 167      28.980  24.460   9.660  1.00  0.00
>
> and following details regarding the error,
>
> Identified residue MET1 as a starting terminus.
> Warning: Residue SEP167 in chain has different type (Other) from starting
> residue MET1 (Protein).
> Warning: Residue ASN168 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue PHE169 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue ALA170 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue VAL171 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> More than 5 unidentified residues at end of chain - disabling further
> warnings.
> Identified residue GLN166 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     MET1  HIS122  CYS127  MET155  HIS181  CYS232
>                      SD5  NE2953   SG987  SD1198 NE21417  SG1802
>   HIS122  NE2953   0.896
>   CYS127   SG987   2.406   2.338
>   MET155  SD1198   2.631   2.424   0.726
>   HIS181 NE21417   2.143   2.161   2.124   1.774
>   CYS232  SG1802   2.805   3.428   3.766   3.748   2.309
>   HIS273 NE22097   4.614   4.982   4.609   4.323   3.017   2.266
> Start terminus: NH3+
> End terminus: COO-
> Checking for duplicate atoms....
> Now there are 283 residues with 2821 atoms
> Making bonds...
> Number of bonds was 2866, now 2861
> Generating angles, dihedrals and pairs...
> Before cleaning: 4579 pairs
>
> -------------------------------------------------------
> Program pdb2gmx_d, VERSION 4.5.1
> Source code file: pgutil.c, line: 88
>
> Fatal error:
> Atom N not found in residue seq.nr. 1 while adding improper
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Thanking you.
>
> With regards,
> Jignesh Patel
>
>
>
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