AMBER Archive (2006)

Subject: RE: AMBER: prepin file nan

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Nov 28 2006 - 15:47:03 CST

Hi,
You may manually modify the atom name and atom type, then run parmchk to find the missing parameters and provide proper values for them (most bond length and bond angle parameters may be obtained through ab initio calculations).

However, if Zn is not covalently bonded to other atoms, I would like to suggest you make Zn itself a residue.

Best

Junmei

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Fenghui Fan
Sent: Tuesday, November 28, 2006 8:49 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: prepin file nan

Hi

If in the input file there is a Zn, and the
antechamber cannot recognize Zn so it gives the nan
for zn, what should we do then?

Best regards.

Fenghui Fan

--- linfu <linfu3200_at_mail.sioc.ac.cn> wrote:

> hi Fenghui Fan
> it seems that antechamber cannot recgonize the para. correctly.
> S1, you can try newly updated version of
> antechamber.
> S2, you can try to use mol2 file to generate the
> prepin.
> hope it can help
>
> Fu Lin
>
> ======= 2006-11-28 11:28:16 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
>
> >Dear all,
> >
> >How can we avoid nan in the prepin file?
> >
> >If there is really nan in the prepin file, what
> kinds
> >of action should we take?
> >
> >If there is really nan in the prepin file, how does
> it
> >influence the frcmod file?
> >
> >I am looking forward to getting your reply.
> >
> >Best regards.
> >
> >Fenghui Fan
> >
> >
> >
> >
>
>_______________________________________________________________________
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>
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
> Àñ£¡
>
>
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡linfu ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡linfu3200_at_mail.sioc.ac.cn
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-11-28
>
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