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. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
