Re: [AMBER] problems with input file preparation

From: sunyeping <>
Date: Sun, 29 Jan 2017 13:39:27 +0800

Hi, thank you for your reply.I find by increasing the number of minimization steps from 2000 to 75000, the equillibrum simulation can be continued after minimization in NAMD now. However, the forces in the system, especially dihedral potential, are still large compared with simulation with CHARMM force field (dihed 5000 vs 1700 kcal/mol). I am not sure whether the production simulation could be extended. 
Yeping------------------------------------------------------------------From:Elvis Martis <>Time:2017 Jan 29 (Sun) 13:07To:孙业平 <>; AMBER Mailing List <>Subject:RE: [AMBER] problems with input file preparation
It seems that there are still larges forces on your system because of which system become unstable.
What was your minimization and equilibration protocol?
    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: sunyeping [
Sent: Sunday, January 29, 2017 1:54 AM
To: AMBER Mailing List <>
Subject: [AMBER] problems with input file preparation

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
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 - 22:00:02 PST
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