AMBER Archive (2009)

Subject: Re: [AMBER] atomtypes in gaff

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 25 2009 - 06:45:16 CDT

Quoting "Aust, Susanne" <saust_at_ipb-halle.de>:

Could you send me your LEaP script (that used to generate your
prmtop/prmcrd files) + Zinc library (mol2 file format) + FF library
for your benzimidazole-structure (mol2 file format) + the structure of
your complex (PDB file format).

regards, Francois

> I load the complex in xleap as pdb, so no name is necessary.
> At my first trail I load the wrong pdb with ZNB in the pdb. I correct this to
> ZNA (like in my ZNA.lib) and load the pdb again and then everything was read
> in without error.
> The ligand in the complex has the name ABI. The parameter for this ligand I
> read in to xleap with loadamberparams bzim_correct.frcmod and loadamberprep
> bzim_correct.prepin.
> When I prepare my complex in xleap, there is no error and the pdb or mol2
> from xleap looks o.k.
> But after the minimization the ligand is not coordinated. With a wrong
> benzimidazole-structure (the double bonds are not on the correct positions)
> the ligand keeps coordinated.
> It's difficult for me, to describe the problem, because I don't know exactly
> at which position of the preparation line the failure occurs.
> regards,
> Susanne
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]Im
> Auftrag von FyD
> Gesendet: 25 June 2009 12:33
> An: AMBER Mailing List
> Betreff: Re: AW: [AMBER] atomtypes in gaff
>
>
> 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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           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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