AMBER Archive (2009)

Subject: Re: [AMBER] Zinc

From: Roman Osman (roman.osman_at_mssm.edu)
Date: Tue Sep 29 2009 - 19:08:28 CDT


Try this:
http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
it's the best Zn force field for amber.

On Sep 29, 2009, at 5:31 PM, Rubben Torella wrote:

> Ok the problem for the zinc is that you have to change in the .pdb
> file the
> atom name form ZN to ZNA... try in this way!
> For the other aminoacid, if ASP is not terminal, you have to change
> the atom
> name...
>
> 2009/9/29 Sel Ercan <slmrcn_at_ymail.com>
>
>> Hi all.
>> I want to minimize 1WJD.pdb (hiv-1 integrase n-terminal domain).
>> Loading
>> pdb to xleap gives error about Zinc.
>> Xleap gives these three errrors:
>> FATAL: Atom .R<HIE 12>.A<HD1 18> does not have a type.
>> FATAL: Atom .R<ASP 55>.A<OXT 13> does not have a type.
>> FATAL: Atom .R<ZN 56>.A<ZN 1> does not have a type.
>> can anyone tell me what to do? Is there any force field for zinc?
>>
>>
>>
>>
>> _______________________________________________
>> 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

Roman Osman
roman.osman_at_mssm.edu

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