Re: AMBER: antechamber problems

From: Shulin Zhuang <shulin.zhuang.gmail.com>
Date: Tue, 21 Jun 2005 09:07:56 +0800

Dear Wang,

You say that different algorithms were used to assign bond types in
amber7 and amber8.

I use RESP method to produce the prepi and frcmod file. In amber8, I
use the same procedure of RESP method as that in amber7. Is it ok?

Both in amber7 and amber8, I perform the following procedure:

after generation of the Gauss output file(lig.out):

1. antechamber -nc -1 -o lig.ac -fo ac -i lig.out -fi gout -c resp

2. atomtype -i lig.ac -o lig_gaff.ac -p gaff

3. antechamber -fi ac -fo prepi -i lig_gaff.ac -o lig.prepi

4. parmchk -i lig.prepi -fi prepi -o frcmod

Is this procedure appropriate for amber8 too?

By the way, after generation the prepi and frcmod file, I use ff03
force filed and gaff to generate the complex prmtop and inpcrd files
with amber8 in SGI300.

Because the SGI300 of our lab just has 4 cpu and the amber8 package is
not parallized in this workstation, I have to perform minimization
and following MD in Linux cluster using amber7. Is this
practiceable?

Best regards


-- 
   Shulin Zhuang
Chemistry Department 
Zhejiang University PRC
shulin.zhuang.gmail.com
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Received on Tue Jun 21 2005 - 02:53:00 PDT
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