[gmx-users] TP2 problem

Justin Lemkul jalemkul at vt.edu
Tue Jan 2 13:58:22 CET 2018

On 1/2/18 7:54 AM, farial tavakoli wrote:
> Dear GMX users
> I need to generate a topology for my complex (protein + peptide) using CHARMM36 ff in gromacs , since It has 2 phosphotyrosine residues. I did these steps:
> at first , I converted TYR in pdb file to TP2, accordingly the merged.tpr file of CHARMM36 ff.
> then , changed P atom in pdb file to P1 and changed O1P,O2P,O3P in pdb file to O2,O3,O4 , respectively, in accord with merged.tpr file
>   added TP2 residue to residuetype.dat file as a protein in working directory
> My protein has 323 residues , start terminus: GLY 1  and  end terminus : ILE 323My peptide has 7 residues , start terminus : THR 1  and  end terminus :  PRO 7
> but when issued this command:
>   gmx pdb2gmx -f .pdb -o .gro -ignh -water tip4p
>   faced to this error and warnings:
> Start terminus GLY-1: GLY-NH3+
> End terminus ILE-323: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 323 residues with 5204 atoms
> Chain time...
> Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.14#
> Making bonds...
> Number of bonds was 5261, now 5261
> Generating angles, dihedrals and pairs...
> Before cleaning: 13845 pairs
> Before cleaning: 14000 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are  321 cmap torsion pairs
> There are 14000 dihedrals,  863 impropers, 9560 angles
>            13764 pairs,     5261 bonds and     0 virtual sites
> Total mass 36882.800 a.m.u.
> Total charge -7.000 e
> Writing topology
> Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.14#
> Processing chain 2 'B' (73 atoms, 7 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
>   protonation. 12 donors and 10 acceptors were found.
> There are 11 hydrogen bonds
> Will use HISE for residue 2
> Identified residue THR1 as a starting terminus.
> Warning: Residue TP23 in chain has different type (Other) from starting residue THR1 (Protein).
> Warning: Residue TP24 in chain has different type (Other) from starting residue THR1 (Protein).
> Warning: Residue LEU5 in chain has different type (Protein) from starting residue THR1 (Protein).
> Warning: Residue LEU6 in chain has different type (Protein) from starting residue THR1 (Protein).
> Warning: Residue PRO7 in chain has different type (Protein) from starting residue THR1 (Protein).
> Identified residue HIS2 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus THR-1: NH3+
> End terminus HIS-2: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2016.4
> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
> Fatal error:
> Atom OXT in residue PRO 7 was not found in rtp entry PRO with 14 atoms
> while sorting atoms.
> .
> For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> I am confused and dont understand where the problem is? It has taken my time for 2 days. I would really appreciate it if anybody helps me to solve this problem.
> best regardsFarial

Three people have asked identical questions within the last day. Please 
pay attention to other posts that are on similar topics so we can avoid 
repeating ourselves.

The issue is that you do not have TP2 in residuetypes.dat and properly 
identified as Protein (note the messages above about chain 
discontinuities). Add this and pdb2gmx will work.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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