This issue has been solved by the below corrections
chamber -top ./toppar/top_all36_prot.rtf -param ./toppar/par_all36_prot.prm
-psf step1_pdbreader.psf -crd step1_pdbreader.pdb -str
./toppar/par_all36_cgenff.prm ./toppar/p0g.prm -nocmap
Now converting 2 psf files I obtain 2 prmtop files corresponded to the 1)
solvated complex included membrane and 2) dry complex of protein-ligand
atoms only.
Taking as the input dry complex I'd like to create 2 additional prmtops for
the ligand and protein separately using
ante-MMPBSA.py -p complex_dry.prmtop -r receptor -l ligand -n
How I should specify ligand mask properly ? E.g I ligand is the 1 residues
with the name p0g. Trying ante-MMPBSA.py -p complex_dry.prmtop -r receptor
-l ligand -n p0g
I've obtained 2 identical prmtops for the ligand and receptor.
James
2014-04-22 13:49 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> 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 - 04:00:02 PDT
