Hi Jason,
I am facing another problem. The new .prmtop file which I generated using
chamber is not compatable with NAMD. The NAMD program showing some error
like
Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Failed to read AMBER parm file!
Charm++ fatal error:
FATAL ERROR: Failed to read AMBER parm file!
However, when I generate a file using tleap then it is running. But during
that time I need to use amber force filed which I don't want. Please give
some suggestions how do I use chamber generated .prmtop file for runnig
namd2 or mmpbsa.py program. Is there any tricks or do I need to change
format further? if so, how can I do that?
best
sudipta
On Sat, Sep 14, 2013 at 10:28 PM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi Jason,
>
> I can create the prmtop file without any error using chamber. I have made
> all the prmtop file using chamber and converted my namd .dcd file to .mdcrd
> rajectory file. However, there is some problem to run it. The errors are
> following below.
> time MMPBSA.py -O -i mmpbsa_ptraj.in -o FINAL_RESULTS_MMPBSA_NMODE.dat
> -sp 3jzb_test.prmtop -cp 3jzb_complex.prmtop -y
> 3jzb_protein_ligand_system_12.mdcrd
> Loading and checking parameter files for compatibility...
> ValueError: invalid literal for int() with base 10: '8('
> Exiting. All files have been retained.
>
>
> On Sat, Sep 14, 2013 at 7:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Sat, Sep 14, 2013 at 2:55 PM, sudipta <sudipta.mml.gmail.com> wrote:
>>
>> > Hi Ross,
>> >
>> > I have generated charm formatted psf file using charmm progarm. The
>> chamber
>> > program successfully reads that .psf file. Moreover, it also finds the
>> > right atom types and nonbonded parameters. After that, I am getting some
>> > strange errors. I don't understand the details of that errors. Please
>> help
>> > me out in this regard. The output looks like
>> >
>> > | *****************************************************
>> > | * CHAMBER: Charmm psf to AMBER prmtop convertor *
>> > | * *
>> > | * v1.0 *
>> > | * *
>> > | * Written by: *
>> > | * Mark J. Williamson *
>> > | * Michael F. Crowley *
>> > | * Ross C. Walker *
>> > | * *
>> > | *****************************************************
>> >
>> > EXTented file format is being used
>> >
>> > ===========================================================
>> > PSF input parsing summary
>> > ===========================================================
>> >
>> > Number of PSF flags found: 4
>> >
>> > Number of atoms found: 70725
>> > Number of residues found: 22432
>> >
>> > Number of bonds found: 70758
>> > Number of angles found: 29949
>> > Number of dihedrals found: 11405
>> > Number of impropers found: 693
>> >
>> > Number of donors found: 443
>> > Number of acceptors found: 22558
>> > Number of explicit nonbonded exclusions found: 0
>> >
>> > Number of groups found: 23413
>> > Number of ST2 waters found: 0
>> >
>> > Number of cross terms found: 261
>> > ===========================================================
>> >
>> > --- Found all ATOM TYPES in topology file
>> >
>> > --- Found all nonbond parameters
>> > At line 641 of file psfprm.F90
>> > Fortran runtime error: Bad value during floating point read
>> >
>> > By the way my system contains protein and ligand and they have their own
>> > separate parameter and topology files. I just combined them by cat
>> command
>> > and make a single file. Is there any wrong with it?
>> >
>>
>> I do not think you can simply concatenate two PSF files (you certainly
>> cannot do that with two PRMTOP files).
>>
>> I believe you need one PSF file for the combined system. Also,
>> ante-MMPBSA.py will not work with chamber topology files, so you will need
>> to make sure that you make each one that you need using chamber.
>>
>> 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 15 2013 - 22:00:02 PDT
