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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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