AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 25 2009 - 06:36:20 CDT

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

> 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.

Could you send me the mol2 file of another complex with another ligand
and the same protein where the ligand remains complexed to the Zinc
after geometry optimization.

regards, Francois

> -----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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber