[gmx-users] what's the pdb file format containing five peptides?
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 6 07:31:50 CEST 2008
> Hi! everyone,
> I am simulating a system containing 5 peptides and a popc membrane.When I use
> pdb2gmx,I get this warning:
> Fatal error:
> Atom H1 in residue GLY 38 not found in rtp entry with 5 atoms
> while sorting atoms. Maybe different protonation state.
> Remove this hydrogen or choose a different protonation state.
> Option -ignh will ignore all hydrogens in the input.
> My peptide has 37 residues.I think 38residue is another peptide's first
> residue.Its chain number is 2 I am writting in pdb file.It is showing that pdb2gmx
> only read one peptide.How I amend my pdb file to make pdb2gmx can read five
> peptides? Please help me.Your advice is appreciated.Thank you!
Did you use option -ignh as the error message suggests?
If your chains are all labeled correctly it should work.
> Best regards.
> china HuaZhong Normol University
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
More information about the gromacs.org_gmx-users