Jason,
chamber -top ./toppar/top_all36_prot.rtf -param ./toppar/par_all36_prot.prm
-psf step1_pdbreader.psf -crd step1_pdbreader.pdb -nocmap -str
./toppar/par_all36_cgenff.prm ./toppar/p0g.prm
resulted in
Error unknown flag: ./toppar/p0g.prm
Some bug?
James
2014-04-22 13:42 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
>
> On Apr 22, 2014, at 4:54 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> Jason,
>
> I've faced with the problems during conversion of the psf's to the prmtop.
>
> 1) Trying converting VMD's xplor psf I've obtained error
> At line 3316 of file psfprm.F90 (unit = 20, file = '1ZGO_m2_ion.psf')
> Fortran runtime error: Bad value during integer read
>
> 2) Trying converting charmm's psf's I've faced with the problem of multi
> prm files. This time I've used Charm-gui output consisted of
> receptor-ligand complex embedded in the membrane so the topology and
> parameters of this system has been divided on several prm and inp files.
> This time I've made succesfull convertion on the protein only using 1 prm
> file but obtained below error in case of conversion of the enterily system
> providing 2 additional prm's by means of -str flag
>
> chamber -top ./toppar/top_all36_prot.rtf -param
> ./toppar/par_all36_prot.prm -psf step4_lipid.psf -crd step4_lipid.pdb
> -nocmap -str ./toppar/par_all36_lipid.prm -str
> ./toppar/toppar_water_ions.str
>
>
> Take out the second -str flag. The stream files should be specified
> continuously after a single -str flag.
>
>
> <get_atom_parameters> ERROR, topology file(s) ends without finding all
> atom types,
> number found: 58 needed ntypes: 60
>
> in this case the parameters from the last (water and ions) files have not
> been written. How such multi inputs should be provided correctly?
>
> James
>
>
>
> 2014-04-21 18:36 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Mon, 2014-04-21 at 18:32 +0400, James Starlight wrote:
>> > Jason,
>> >
>> >
>> > many thanks for suggestions. The problems was exactly in the root
>> > permissions. By the way from the amber manual I've noticed that in new
>> > realize 3 different way's of MMPBSA calculations are realized. In this
>> > regard I wounder to know 1) if the existing MMPBSA on-line tutorial is
>> > still valid
>>
>> Yes, it's still valid.
>>
>> > and 2) what exactly MMPBSA method could be better for my task
>> > (analysis of the namd produced dcd trajectories with the conversion of
>> > the psf topologies to amber format)?
>>
>> I suggest using MMPBSA.py. It supports DCD trajectories (as well as
>> every other trajectory format cpptraj recognizes) directly and generally
>> receives more support on the mailing list.
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>
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Received on Tue Apr 22 2014 - 03:00:02 PDT
