Tue Oct 13 11:54:04 CEST 2015

On 10/13/15 5:52 AM, himanshu khandelia wrote:
> 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?
>

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

Step 5.

-Justin

>
>
> * 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.
>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================