[gmx-users] error in running pdb2gmx

[Justin Lemkul]

On 11/18/13 6:10 AM, hasthi wrote:
> Dear Justin,
>                   Thank you for your reply. Yeah I have modified my force
> field to include the phosphorylated Serine residue.
> Below is the pdb2gmx command employed
>
> pdb2gmx -f alpha_ser129p.pdb -o alpha_sep129p.gro -ff gromos43a1 -ignh
>
> error :
> Fatal error:
> Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
> while sorting atoms.
>
> snippet of my PDB file.
> ATOM   2011  N   ALA A 140     205.034 -53.935 -18.851  1.00
> 16.70           N
> ATOM   2012  CA  ALA A 140     204.971 -52.762 -19.777  1.00
> 17.17           C
> ATOM   2013  C   ALA A 140     203.730 -51.927 -19.454  1.00
> 17.37           C
> ATOM   2014  O   ALA A 140     202.844 -52.453 -18.799  1.00
> 17.40           O
> ATOM   2015  CB  ALA A 140     204.885 -53.253 -21.221  1.00
> 17.38           C
> ATOM   2016  OXT ALA A 140     203.683 -50.781 -19.870  1.00
> 17.61           O1-
> ATOM   2017  H01 ALA A 140     204.210 -54.107 -21.275  1.00
> 17.38           H
> ATOM   2018  H02 ALA A 140     204.184 -54.311 -18.455  1.00
> 16.70           H
> ATOM   2019  H03 ALA A 140     205.867 -52.154 -19.652  1.00
> 17.17           H
> ATOM   2020  H04 ALA A 140     205.876 -53.550 -21.564  1.00
> 17.38           H
> ATOM   2021  H05 ALA A 140     204.507 -52.451 -21.855  1.00
> 17.38           H
>
>
> Besides this I also find the following lines in my output:
> Identified residue MET1 as a starting terminus.
> Warning: Residue SEP129 in chain has different type (Other) from starting
> residue MET1 (Protein).
> Warning: Residue GLU130 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue GLU131 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue GLY132 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue TYR133 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 PRO128 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                      MET1    MET5   HIS50  MET116
>                       SD7    SD41  NE2360   SD817
>      MET5    SD41   1.034
>     HIS50  NE2360   5.849   5.344
>    MET116   SD817   7.199   7.369  10.906
>    MET127   SD905   8.542   8.838  12.786   2.065
> Start terminus MET-1: NH3+
> End terminus PRO-128: COO-
>
> Why is the end termini is at Pro 128? Does it mean it does not consider the
> rest of the residues?? Please explain me regarding this.
>

This is the problem:

Warning: Residue SEP129 in chain has different type (Other) from starting
residue MET1 (Protein).

I bet SEP is a phosphorylated serine that you or someone else has added to the 
force field, but forgot step #5 here:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Without the proper specification of residue type, pdb2gmx thinks it is a 
discontinuous chain.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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