Re: [AMBER] error massage in constant pH simulation

From: Jason Swails <>
Date: Tue, 6 Jul 2010 08:53:07 -0400


Your errors are MPI errors, and it doesn't look like sander is running
properly. Did you run the parallel sander tests successfully?

I do have a comment about your input file: did you heat and equilibrate
first? If so, you are using ntx=1 and irest=0, which means you are ignoring
all velocity information in your restart file, which would be there if you
heated and equilibrated. You should set ntx=5 and irest=1. If you didn't
heat/equilibrate, you should definitely do that.

Also, loadamberparm should be loadamberparams in your leap script. If an
mdout file was created, that file probably has a more helpful error message
than your stderr stream, so you may consider including that in your next

Hope this helps,

On Tue, Jul 6, 2010 at 5:16 AM, nicholus bhattacharjee <> wrote:

> Dear community,
> I am doing a constant pH simulation of a protein.
> I have prepared the necessary files in my system (a desktop) having Amber 9
> installed in it while I am running the simulation in a remote cluster
> having
> Amber 10 installed (Don't know the problem might be due to different
> version).
> Bellow is the procedure I followed while preparing the files necessary for
> constant pH simulation
> I have change ASP & ASH into AS4, GLU & GLH into GL4 and HIS,HID & HIE into
> HIP in my pdb file.
> $ tleap
> >source leaprc.ff99SB
> >set default PBRadii mbondi2
> >loadoff constph.lib
> >loadamberparm frcmod.constph
> >mol=loadpdb my.pdb
> >charge mol
> Total unperturbed charge: -5.003600
> Total perturbed charge: -5.003600
> >addions mol Na+ 0
> >saveamberparm mol prmtop inpcrd
> >quit
> Since I am doing the simulation at pH 3 I have exclude TYR and LYS from
> cpin
> file
> $ ambpdb -p prmtop <inpcrd | -notresname TYR, LYS> cpin
> I am sending the input and error files as attachment. Please tell me what
> is
> the problem.
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jul 06 2010 - 06:00:03 PDT
Custom Search