Tue Oct 13 11:52:03 CEST 2015

Dear All

I am using pdb2gmx to read a pdb file containing a dianionic
phosphotyrosine (residue TP2 in charmm36)

However, for some reason, pdb2gmx detects a c-terminus right before the
residue TP2, resulting in a crash. Is TP2 a residue name reserved for a
C-terminus or something?

I have checked the residue numbering and the file format. It is all
correct.

Any suggestions?

* Here is the command:
gmx_mpi pdb2gmx -f xxx.gro -water tip3p -ignh

(and then choosing the charmm36 force field, option 9)

* the output error:

Start terminus GLY-565: GLY-NH3+
End terminus ASN-822: COO-
Opening force field file
/home/hkhandel/bin/gmx/gromacs5.1/share/gromacs/top/charmm36-jun2015.ff/merged.arn

-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hkhandel/DOWNLOADS/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2gmx.c,
line: 746

Fatal error:
Atom OXT in residue ILE 935 was not found in rtp entry ILE with 19 atoms
while sorting atoms.

(NOTE THAT 935 IS THE LAST RESIDUE IN THE PDB FILE, AND NOT 822)

* section of pdb file near residue 823:

 822ASN   HD22 4035   4.781   6.337   4.984
  822ASN      C 4036   5.058   6.726   4.716
  822ASN      O 4037   5.168   6.779   4.727
  823TP2      N 4038   4.949   6.798   4.680
  823TP2     HN 4039   4.861   6.753   4.670
  823TP2     CA 4040   4.951   6.942   4.659
  823TP2     HA 4041   5.038   6.984   4.707
  823TP2     CB 4042   4.951   6.982   4.509
  823TP2    HB1 4043   5.032   6.928   4.456
  823TP2    HB2 4044   4.855   6.953   4.461
  823TP2     CG 4045   4.975   7.130   4.489
  823TP2    CD1 4046   5.102   7.185   4.510
  823TP2    HD1 4047   5.184   7.121   4.541
  823TP2    CE1 4048   5.124   7.323   4.494
  823TP2    HE1 4049   5.222   7.365   4.511
  823TP2     CZ 4050   5.019   7.406   4.454
  823TP2     OH 4051   5.039   7.545   4.438
  823TP2     P1 4052   5.088   7.629   4.549
  823TP2     O2 4053   5.226   7.679   4.551
  823TP2     O3 4054   4.989   7.748   4.579
  823TP2     O4 4055   5.065   7.549   4.683
  823TP2    CD2 4056   4.871   7.215   4.449
  823TP2    HD2 4057   4.772   7.174   4.434
  823TP2    CE2 4058   4.892   7.352   4.431
  823TP2    HE2 4059   4.809   7.415   4.401
  823TP2      C 4060   4.827   7.002   4.726
  823TP2      O 4061   4.718   6.946   4.719
  824VAL      N 4062   4.842   7.118   4.793
  824VAL     HN 4063   4.934   7.156   4.804
  824VAL     CA 4064   4.734   7.195   4.853
  824VAL     HA 4065   4.681   7.129   4.920
etc.

-- 
-------------------------
Himanshu Khandelia, PhD
Associate Professor
MEMPHYS, Center for BioMembrane Physics: www.memphys.dk/Himanshu-Khandelia
University of Southern Denmark (SDU)
Campusvej 55, Odense M 5230, Denmark
Phone: +45 6550 3510, +45 2912 5467
In India: +917893140837
email: hkhandel at sdu.dk <hkhandel at memphys.sdu.dk>, hkhandelia at gmail.com
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