[gmx-users] NH2 IN CTERMINAL

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:
> Dear justin
> Hi,
> In my simulation with ff53a5 when I do this command  pdb2gmx  -f
> name.pdb  -ter  -ignh -water spce .I find this error .C-terminus: None
> Now there are 14 residues with 138 atoms
> Making bonds...
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Number of bonds was 142, now 139
> Generating angles, dihedrals and pairs...
> Before cleaning: 210 pairs
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.2
> Source code file: pgutil.c, line: 87
> 
> Fatal error:
> Atom H not found in residue 14 while adding improper
> 
> how can resolve this problem?

I'm assuming you're using -ter to add some sort of capping group to the 
C-terminus.  It seesms that there is some inconsistency between your structure 
nomenclature for this atom and that which is expected by the .rtp/.tdb file.

-Justin

> 
> best regards

-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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