[AMBER] problems with input file preparation

From: sunyeping <sunyeping.aliyun.com>
Date: Sun, 29 Jan 2017 04:23:56 +0800

Dear all,
I am learning to use amber to do MD simulation. I prepared my input files with tleap with the following script:
source /app/build/amber16/dat/leap/cmd/oldff/leaprc.ff99SB
mol=loadpdb ABPK_new.pdb
desc mol #list residue numbers
bond mol.101.SG mol.164.SG
bond mol.203.SG mol.259.SG
bond mol.301.SG mol.356.SG
check mol
solvatebox mol TIP3PBOX 10
charge mol
addIons2 mol Na+ 0
saveAmberParm mol ABPK_wb_ion.prmtop ABPK_wb_ion.inpcrd
The input files "ABPK_wb_ion.prmtop" and "ABPK_wb_ion.inpcrd" generated  by this script were attached at https://www.dropbox.com/sh/hx3z3xkwvmp6nqa/AABNgRyeqt3guDKvA0oEwahqa?dl=0
I don't have amber sander installed in my system so I tried to do my simulation with NAMD. I began the simulation with a minimization step followed by a equllibrium simulation with CA atom constraint, but just when the minimization is finished and the system began to be heating, the error occur with the following error message:
ERROR: Constraint failure in RATTLE algorithm for atom 2581!
ERROR: Constraint failure; simulation has become unstable.

I don't know whether the problem is caused by the input top and coord files or parameters in the NAMD configure file. Could anyone do me a favor to perform a minimization and a short production simulation with AMBER to check whether these input file could work? If they can not, what are the problems with them?Thank you in advance!
Yeping Sun
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Received on Sat Jan 28 2017 - 12:30:02 PST
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