AMBER Archive (2009)

Subject: Re: AW: [AMBER] atomtypes in gaff

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 25 2009 - 05:32:33 CDT

Susanne,

You need to add a molecule name to your Tripos mol2 file (I wonder if
this is not a bug in the savemol2 command because you have many
residues...):
@<TRIPOS>MOLECULE
C2K
  3263 3293 228 0 1
SMALL
etc...

> The atomtypes should be correct.
> I send you the mol2 file of the comlex from xleap.
> The benzimidazole is over the N3 (nd) non physical coordinated to the zinc.
> I calculate other ligands (substrate and imidazole derivative) with this
> enzyme and it works.
> So I think it is not a problem of zinc.
> I hope, this is the file you want.
> I send you also the xleap.log

In your LEaP log file, you load the Zinc FF library:
loadoff ZNA.lib

In your Tripos mol2 file, your Zinc is defined as ZNB (residue name,
FF atom type & atom name). Consequently, in LeaP you get this message:

Unknown residue: ZNB number: 225 type: Terminal/last
..relaxing end constraints to try for a dbase match
   -no luck
(Residue 226: ZNB, Terminal/last, was not found in name map.)
Unknown residue: ZNB number: 226 type: Terminal/last
..relaxing end constraints to try for a dbase match
   -no luck

Then, you load the frcmod file for your zinc atom:
Loading parameters: ./frcmod.zna
Reading force field modification type file (frcmod)
Reading title:
This frcmod file is for ZNA (zinc 2+ ion).
(UNKNOWN ATOM TYPE: ZNA)

I wonder if the FF atom type of Zn is well defined.

=> add
addAtomTypes {
          { "ZN" "Zn" "sp3" }
           ^^^^
      or what is required...
}

I do not know if these are the reasons of your problem. However, you
might correct these problems to see if this helps.

regards, Francois

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