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

[Mark Abraham]

On 18/06/2011 1:13 AM, udaya kiran marelli wrote:
> 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)

With -ignh you told it to strip away all the H atoms, and that requires 
that pdb2gmx knows how to rebuild them (or doesn't need to know).

> -------------------------------------------------------
> 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.

If you mean that the the cyclization is achieved with a peptide bond 
from "N-terminal" N to "C-terminal" C, you will have to use the 
specbond.dat mechanism to achieve that. See chapter 5.

The problem arises because HN is defined in the .hdb in terms of C in 
the preceding residue, which is not applicable in your case, because 
there is not a regular peptide bond.

Rather than the "brute force" -ignh mechanism, there may be a better 
approach (like removing particular offending hydrogen atoms from your 
input coordinate file) that doesn't require pdb2gmx to need to know how 
to rebuild HN.

Mark

> 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 <tel:%2B49-%280%2989-289-13760>
> Fax: +49-(0)89-289-13210 <tel:%2B49-%280%2989-289-13210>
> email: kiran.udaya at tum.de <mailto:kiran.udaya at tum.de>
>

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