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
