[gmx-users] cyclic peptide on GROMACS compatoble with Charmm (all-atom) force field

[udaya kiran marelli]

 Dear GROMACS users,

I am trying to construct a cyclic hexa peptide containing all Ala residues.
 During pdb2gmx conversion using the command    (pdb2gmx -ff charmm27 -ignh
-f TESTALA.pdb -o TESTALA.gro -ter)  it gave the following error while I am
demanding the program to give uncharged termini (option :  None)

WARNING: atom HN is missing in residue ALA 1 in the pdb file
        You might need to add atom HN to the hydrogen database of residue
ALA
        in the file ff???.hdb (see the manual)


-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2top.c, line: 704

Fatal error:
There were 1 missing atoms in molecule Protein, if you want to use this
incomplete topology anyhow, use the option -missing

In the .hdb file the atom HN is defined already.  The error is that it is
removing the #HN# atom from the Ala 1 residue at the cyclization point.

Could you suggest me in getting rid off the problem.


yours sincerely
Uday.

Marelli Udaya Kiran
C/o.  Professor Dr. Horst Kessler
Institute for Advanced Study
Department Chemie
Technische Universität München
Lichtenbergstrasse 4
D-85747 Garching, Germany

Tel.: +49-(0)89-289-13760
Fax: +49-(0)89-289-13210
email: kiran.udaya at tum.de
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