[gmx-users] ffg53a5

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 27 09:59:42 CEST 2008

Hi sh-karbalaee,

Do you have some .itp files you include? Can you track 'HO' in there?

If all else fails, write out the full (preprocessed) topology file,
using the option -pp of grompp and search there (although I'd still
bet it's in one of the .itp files).



On Wed, Aug 27, 2008 at 8:27 AM, shahrbanoo karbalaee
<shahrbanoo at gmail.com> wrote:
> Dear justin
> I cannot find my error.I make mix solvent tfe and spc  ( was
> minimized)and solvate on  a peptide.I use ffg53a5 .I take this error
> .I saw in line 61 in top file but there is not  Ho  in top file and
> rtp file ffg53a5. what do i de?please help me.
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> Cleaning up temporary file gromppIpCYKg
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: toputil.c, line: 61
> Fatal error:
> Atomtype 'HO' not found!
> best regards
> --
> sh-karbalaee
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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