AMBER Archive (2007)

Subject: Re: AMBER: topology for postprocessed files?

From: anna.schrey_at_gmx.de
Date: Wed Apr 18 2007 - 12:40:51 CDT

-------- Original-Nachricht --------
Datum: Thu, 12 Apr 2007 12:07:08 +0200
Von: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
An: amber_at_scripps.edu
Betreff: Re: AMBER: topology for postprocessed files?

> Dear Anna,
>
> You can create a pdb file with your stripped system and reload it into
> Leap and save the new topology file ...\
> As for the energies, you can do a single step calculation with sander on
> the snapshot(s) that you are interested in ..

dear Vlad,

try to do the following:

cat << eof > anal.in

# no resttraints
 &cntrl
   imin=5,
   ntx=1, irest=0,
   ntrx=1, ntpr=0,
   ntwr=0,
   ntwx=0,ntwv=0,
   ntwe=1,
   ntf=2,ntb=1,
   dielc=1,cut=8,
   scnb=2,scee=1.2,
   ntr=0,nstlim=600000,
   dt=0.002,temp0=300,
   ntt=1,
   tautp=1.0,ntc=2,
  &end
 &wt type='END' &end
eof
sander -O -i anal.in \
-o energy.out -p ../PRGR_B_HPR_wat_ions.top \
-c ../PRGR_B_HPR_NTV_1200ps.mdcrd \
-inf energy.inf -e energy.mden

/bin/rm anal.in

get error message:

forrtl: info: Fortran error message number is 64.
forrtl: warning: Could not open message catalog: ifcore_msg.cat.
forrtl: info: Check environment variable NLSPATH and protection of /usr/lib/ifcore_msg.cat.

What does this mean?

Thanks,

Anna
>
> Best
> vlad
>
>
>
> anna.schrey_at_gmx.de wrote:
>
> >Deas Amber community,
> >
> >I would like to postprocess trajectories that way that I have to remove
> cetrain residues (e.g. a ligand) and calculate the energies afterwerds. The
> trajecotries are no problem, they can be modified that way using ptraj. But
> how to get the corresponding topology file? And how can I calculate the
> energies (e.g. E_el and E_vdw) with SANDER?
> >
> >kind regards,
> >
> >Anna
> >
> >
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
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> Amtgericht Mannheim / HRB 337446
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