AMBER Archive (2005)

Subject: Re: AMBER: SO4 prep file

From: scopio (scopio_at_163.com)
Date: Tue Jan 18 2005 - 06:57:29 CST

Dear Rai:

If SO4 is buffer ion, I think it can be removed from pdb file in most
cases. Otherwise, if it's necessary for your simulation, you can use
antechamber to generate the parameters.

Hope it helps!

Liu

On Tue, 18 Jan 2005 18:06:42 +0530 (GMT+5:30), Jagdish Rai
<jagdish_at_icgeb.res.in> wrote:

> dear sir
> since i get following message in tleap when preparing prmcrd and prmtop
> for 2RNS (pdb id ). i suppose, the prep file for SO4 is required and may
> be frcmod file also.
> FATAL: Atom .R<SO4 20117>.A<S 1> does not have a type.
> FATAL: Atom .R<SO4 20117>.A<O1 2> does not have a type
> FATAL: Atom .R<SO4 20117>.A<O2 3> does not have a type
> FATAL: Atom .R<SO4 20117>.A<O3 4> does not have a type.
> FATAL: Atom .R<SO4 20117>.A<O4 5> does not have a type.
> please tell me where can get SO4 prep file
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu