[gmx-users] about POPC in Gromacs

[Justin A. Lemkul]

Unknown wrote:
> Hello all:
>   I am a new GROMACS user. I am learning g_membrane in GROMCAS these
> days.
> 
> It is said that the latest CHARMM36 with pre-equilibrium POPC performed
> very well for membrane simulation and I try to use the POPC PDB file in
> the website. http://terpconnect.umd.edu/~jbklauda/research/download.html
> 
> However, when I try to run pdb2gmx for the POPC file in the above link
> with command:
> pdb2gmx -f popc.pdb -o popc_por.gro -water tip3p
> 
> it is said:
> ------------------log-------------------------------------------
> There are 0 hydrogen bonds
> Warning: Starting residue POPC1 in chain not identified as
> Protein/RNA/DNA.
> Warning: Starting residue POPC2 in chain not identified as
> Protein/RNA/DNA.
> Warning: Starting residue POPC3 in chain not identified as
> Protein/RNA/DNA.
> Warning: Starting residue POPC4 in chain not identified as
> Protein/RNA/DNA.
> Warning: Starting residue POPC5 in chain not identified as
> Protein/RNA/DNA.
> More than 5 unidentified residues at start of chain - disabling further
> warnings.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the
> behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Opening force field
> file /soft/gromcas-4.5.4/share/gromacs/top/charmm36.ff/aminoacids.arn
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: pdb2gmx.c, line: 655
> 
> Fatal error:
> Atom H11 in residue POPC 1 was not found in rtp entry POPC with 134
> atoms
> while sorting atoms.
> -------------log-------------------------------------------------
> 
> So, I am  wondering does anybody has any idea about how to solve this
> problem? I would be very appreciated for your such kind helps.
> 
> 

The root of the problem and possible solutions are here:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-Justin

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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