Hi Jason,
I can run a NVT simulation using amber12 with chamber generated .prmtop
file. However, I can't run the MMPBSA.py.MPI program. It shows some error
like
ValueError: invalid literal for int() with base 10: '8('
Error occured on rank 2.
Exiting. All files have been retained.
The command line is
time mpirun -np 8 /home/sudipta/AMBER/amber12/bin/MMPBSA.py.MPI -O -i
mmpbsa_ptraj.in -o FINAL_RESULTS_MMPBSA_NMODE.dat -sp
3jzb_complex_solv.prmtop -cp 3jzb_complex.prmtop -y
3jzb_protein_ligand_system_34.mdcrd > progress_mmpbsa.log
and all the .prmtop files were generated using
/home/sudipta/AMBER/amber12/bin/chamber -top top_all27_prot_na.rtf -top
top_thyroid.inp -param new1.prm -psf 3jzb.psf -crd complex_solv2.pdb -p
3jzb_complex_solv.prmtop -inpcrd 3jzb_complex_solv.inpcrd -cmap -box
88.447 88.447 88.447 -vmd
/home/sudipta/AMBER/amber12/bin/chamber -top top_all27_prot_na.rtf -top
top_thyroid.inp -param new1.prm -psf 3jzb_protein.psf -crd protein.pdb -p
3jzb_protein.prmtop -inpcrd 3jzb_protein.inpcrd -cmap -box 88.447 88.447
88.447 -vmd
/home/sudipta/AMBER/amber12/bin/chamber -top top_all27_prot_na.rtf -top
top_thyroid.inp -param new1.prm -psf 3jzb_ligand.psf -crd ligand.pdb -p
3jzb_ligand.prmtop -inpcrd 3jzb_ligand.inpcrd -cmap -box 88.447 88.447
88.447 -vmd
/home/sudipta/AMBER/amber12/bin/chamber -top top_all27_prot_na.rtf -top
top_thyroid.inp -param new1.prm -psf 3jzb_complex.psf -crd complex.pdb -p
3jzb_complex.prmtop -inpcrd 3jzb_complex.inpcrd -cmap -box 88.447 88.447
88.447 -vmd
and the namd generated .dcd file was converted to .mdcrd file by using the
following command line
/home/sudipta/AMBER/amber12/bin/cpptraj 3jzb_complex_solv.prmtop <ptraj.in
>ptraj.log
where the ptraj.in contains
trajin ../3jzb_protein_ligand_system_34.dcd
trajout 3jzb_protein_ligand_system_34.mdcrd
Can you point out where is my wrong?
Do I need to use ante-MMPBSA.py program for generating the .prmtop file
for running MMPBSA.py.MPI program. If so how do I use that? Is there any
significant difference between AMBERtools12 and AMBERtools13 for running
MMPBSA.py.MPI program
I really appreciate your help.
Thanks in advance
Sudipta
On Sun, Sep 22, 2013 at 10:46 AM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi Jason,
>
> I am facing some difficulty to run amber12 where the .prmtop and .inpcrd
> files were generated using chamber. Strangely, I don't see any box
> information in the inpcrd file and the errors are related with that. Do I
> need that information for running sander.MPI. If so, how do I include that.
> I tried to add that manually but it doesn't work. These are the control
> parameters during that time
>
>
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntt = 3,
> temp0 = 300.0,
> gamma_ln = 2.0,
> ntp = 1,
> taup = 2.0,
> ntb = 2,
> ntc = 2,
> ntf = 2,
> nstlim = 1000,
> ntwe = 100, ntwx = 100, ntpr = 200,
> /
>
>
> The error in log file looks like
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
>
>
>
> Another thing, the sander.MPI works for for minimization. the cntrl
> parameters are given below for minimization
>
> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> igb = 0,
> cut = 12
> /
>
> Finally, my main aim is to use MMPBSA.py.MPI for the chamber generated
> .prmtop file and namd generated .dcd file. I converted the .dcd file to
> .mdcrd file and use that file for that calculation but it doesn't work at
> all.
>
> Please help me out in this regard. How do I solve this issue.
>
> Best
> Sudipta
>
>
>
> On Mon, Sep 16, 2013 at 1:24 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Mon, Sep 16, 2013 at 1:05 PM, sudipta <sudipta.mml.gmail.com> wrote:
>>
>> > Another thing, the chamber generated .prmtop and .inpcrd files can't
>> > produce output with amber 9 sander.MPI. However, it is showing
>> sander.MPI
>> > is running. That means chamber generated files cannot be used with
>> amber 9.
>> > Is it true? Although, it is silly but I want to make sure that.
>> >
>>
>> Correct. chamber was developed after Amber 9. If all you have is Amber 9,
>> you must use the Amber force field (together with NAMD if you wish) in
>> order to use MMPBSA.py.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Sep 22 2013 - 16:30:02 PDT
