[gmx-users] about POPC in Gromacs

Unknown leuven at yeah.net
Sun May 29 10:16:32 CEST 2011


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.





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