[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

??? wrote:
> 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.
> wumin
> china HuaZhong Normol University
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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

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