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.
Regards,
Hasthi
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