[gmx-users] Error in pdb2gmx command (Justin Lemukel)

Justin Lemkul jalemkul at vt.edu
Mon Apr 17 13:41:21 CEST 2017



On 4/17/17 3:24 AM, Yogendra Patel wrote:
> Hello gromacs users,
>
> I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs
> 4.5.5. While running the pdb2gmx to generate the topology, I'm getting the
> error as follows. I have kept the modified rtp file, pdb file and modified
> ffbonded.itp file in my working folder. The rtp file has been named as

Then that's your problem.  Files in the working directory are not being read, 
instead you are reading everything out of $GMXLIB/charmm27.ff, as the pdb2gmx 
output notes.  If you want to modify force field files locally, you must create 
an entire force field directory, modify the files within it, then choose that 
directory when prompted by pdb2gmx.

-Justin

> aminoacids.rtp same as mentioned in gromacs top folder .Please suggest and
> help.
>
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
> Reading i-paa at 30_2.pdb...
> Read 257 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 30 residues with 257 atoms
>
>   chain  #res #atoms
>   1 ' '    30    257
>
> All occupancies are one
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (charmm27)
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
> Residue 43
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
> Residue 47
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
> Residue 59
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
> Residue 63
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.10#
> Processing chain 1 (257 atoms, 30 residues)
> Identified residue PAHb1 as a starting terminus.
> Identified residue PAHe30 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.5
> Source code file: resall.c, line: 581
>
> Fatal error:
> Residue 'PAHb' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>

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

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

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


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