I believe you can convert a pdb to rst format using ptraj:
trajin <pdb filename>
trajout <new rst filename> restart
Note that the keyword for output in rst format is "restart", not "rst" (that
one always gets me :P).
The only potential problem with this is that you will get a big empty set of
velocities in case you wanted those.
Hope that helps,
Brian
On Thu, Sep 22, 2011 at 9:11 AM, Julian Zachmann <
FrankJulian.Zachmann.uab.cat> wrote:
> Hello dear Amber-Users,
>
> I have a question which probably sounds a bit strange:
>
> I am running a sander protocol which is giving me a restart-file every
> NTWR-steps, in my case every 50.000 steps.
>
> This is working well, my question is, whether I could tell sander to write
> a
> rst.file also for step 0 - right at the beginning.
> I know that this file would be the same as my input-pdb so normally this
> doesn't make any sense, but I'm writing some scripts and therefore it would
> be extremely useful for me to have this.
>
> As an alternative, would it be possible to create a rst-file out of a
> pdb-file? This would not be perfect, but help somehow.
>
> All other solutions are more than welcome!
> Thank you very much!
>
> Julian
>
> imin=0,nmropt=1,dielc=80.,
> ntpr=50,ntwr=-50000,ntwx=50000,
> ntb=0,cut=20,vlimit=10,igb=1,
> ntt=3,gamma_ln=1000,nstlim=500000,dt=0.001,
> pencut=-0.001,offset=0.09,
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Thu Sep 22 2011 - 06:30:04 PDT
