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
<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 - 02:00:03 PDT
