Dear Sudipta,
In my experience Chamber expects two extra lines that are not added when using psfgen.
Normally I always have to add these two lines (one line is blank) manually after generating the charmm psf file with psfgen in vmd.
########################
0 0 !NUMLP NUMLPH
########################
When I have a system without CMAP terms (e.g. a pure membrane) these two lines are added at the very end of the pdf file like this:
########################
.
.
.
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0
1 0 !NGRP
0 0 0
0 0 !NUMLP NUMLPH
#########################
For a system with CMAP terms the lines are added as the second last section like this:
#########################
.
.
.
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0
1 0 !NGRP
0 0 0
0 0 !NUMLP NUMLPH
3 !NCRTERM: cross-terms
56 216 218 224 216 218 224 229
239 241 243 261 241 243 261 263
261 263 265 271 263 265 271 276
#########################
Hope this helps.
Kind regards,
Sarah
Den 16/09/2013 kl. 06.45 skrev sudipta <sudipta.mml.gmail.com>
:
> 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 Mon Sep 16 2013 - 00:30:03 PDT
