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.ud...@tum.de
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