Here is the error from sander
Error opening unit 33: File "'dist.RST'" is missing or unreadable
The file dist.RST is present in the folder. So I tried to remove the '
' from the input file. Now it looks like this:
&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 = 5000000, 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
Like this, the simulation fails and it gives the following errors:
For sander:
At line 821 of file nmrcal.F90 (unit = 33, file = 'dist.RST')
Fortran runtime error: Internal namelist read error
And for pmemd:
At line 990 of file nmr_calls.F90 (unit = 33, file = 'dist.RST')
Fortran runtime error: Cannot match namelist object name restraint
Any suggestions?
Fabrício
2012/9/17 Brian Radak <radak004.umn.edu>:
> 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
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Received on Mon Sep 17 2012 - 14:00:03 PDT
