I'm not an expert with either nmropt or pmemd.cuda, but I believe the
module is newly (differently?) implemented in the CUDA code. Perhaps try
running sander or normal pmemd first?
Regards,
Brian
On Mon, Sep 17, 2012 at 4:01 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello. I am trying to set up a umbrella sampling simulation in order
> to calculate the free energy associated with the separation of two
> transmembrane alpha helices. I have tried to modify the sample file
> given in the amber manual in order to change from an angle restraint
> into a distance restraint, using as reference points the COM of both
> helices.
> Here is the md.in file:
>
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 3, csurften = 3, gamma_ten = 17,
> ninterface = 2 taup = 2.0,
> cut = 8.0,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> temp0 = 310.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 1000, ntwx = 1000, ntwr = 10000,
> ig = -1, ioutfm = 1, iwrap = 1
> nmropt=1,
> /
> &wt type='DUMPFREQ', istep1=10 /
> &wt type='END' /
> DISANG='dist.RST'
> DUMPAVE=dist_vs_t.11
>
> And the dist.RST file I have used
>
> &rst restraint = "distance(com(1-33.N,CA,C) com(34-66.N,CA,C)), r1=0.,
> r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
>
> I am trying to run pmemd.cuda. Once type the command pmemd.cuda...etc,
> I get the following error on the mdout file.
>
> Warning: Error opening "Old" file from subroutine OPNMRG
> File = 'dist.RST'
>
> Does this mean that the syntax I have used for the dist.RST file is
> wrong? If so, how would I prepare such simulation?
> Thank you
> Fabrício
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 17 2012 - 13:30:03 PDT
