Re: [AMBER] Problem in not defining the hybridization of a atomtype

From: David A Case <>
Date: Tue, 27 Dec 2016 12:02:14 -0500

On Mon, Dec 26, 2016, A kS wrote:
> In order to simulate a modified residue I have used a perpin and frcmod
> file corresponding to the modification.
> In that prepin and frcmod file I used an new atomtype for an atom Sulphur.
> Like a standard prepin and frcmod file, information regarding this atomtype
> are given in those files except the hybridization state,
> I forgot to add this atomtype in tleap file by using command "AddAtomtype".
> As a result leap gives a warning "Unknown atomtype".
> I am not sure whether this cause any major problem or not, because I think
> necessary parameters for this atomtype, except hybridization state, are
> given in the respective prepin and frcmod files.

Probably safest to re-run things with the AddAtomType command. The
hybridization means very little, but this command also establishes the
element (atomic number). If you atom type begins with "S" or "s", you are
probably OK, but you should probably check the atomic number in the prmtop
file just to be sure.


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Received on Tue Dec 27 2016 - 09:30:02 PST
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