AMBER Archive (2005)

Subject: AMBER: Cluster - input files

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Mon Nov 28 2005 - 04:37:22 CST

Dear Amber Users,
                    I am trying to do MD simulation on cluster of
organic molecules. I have used AMBER5 for the preparation of prmtop amd
prmcrd files for the clusters (64-monomers;around 6500 atoms). Then i
have used AMBER7 program to run a minimization as well as the MD
simulation. it works.(In AMBER5, i have used prep;link;edit procedure to
prepare the prmtop and prmcrd)

To the same cluster of molecules , I have made the input file (prmcrd,
prmtop) using AMBER7. Then i tried to run a minimization as well as a MD
calc. in AMBER7, i am getting the "MAXINT" error with to edit the size.h
value.

To prepare the cluster input file in AMBER7, i have used the following
commands in Xleap,

(1) first way

1. xleap
2. source leaprc.gaff
3. loadAmberPrep prep.in file name of monomer
4. edit res name
5. saveoff res name res name.lib
6. loadoff res name.lib
7. frcmod = loadamberparams frcmod
8. x = loadpdb pdb-file name of the cluster
9. saveAmberParm x prmtop prmcrd
10. quit
 
(2) second way

1. xleap
2. source leaprc.gaff
3. mods = loadamberparams frcmod
4. loadAmberPrep prep.in file name of the monomer
5. resseq = { resname, ........n-resname } ( n-number of monomers)
6. x = loadPdbUsingSeq pdb file name of the cluster resseq
7. saveAmberParm x prmtop prmcrd
8. quit

In both ways, in the co-ordinate files the volume of the box is same by
AMBER7.

But the co-ordinate files from AMBER5 has lower volume than in AMBER7.

is it the reason for the error?

if not, does anyone can give a correct suggestion to prepare a cluster
input files in AMBER7.

thanks
Anand

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