Hello everybody,
I am a newcomer and I am learning how to use XPLOR on small scripts step by
step.
First I generated .psf file for dialanine peptide using this script:
topology
@@TOPPAR:topallhdg.pro
end
segment
name="dialapeptide"
chain
@@TOPPAR:toph19.pep
sequence
Ala Ala
end
end
end
REMARK ALA dipeptide
write structure
output=diala.psf
end
stop
Then I tried to run simple energy minimization with it using this script:
structure @@diala.psf end
parameter @@TOPPAR:parallhdg.pro end
coor @@diala.pdb end
mini powell nstep=50 end
REMARK after 50 steps powell
write coor output=diala_min.pdb end
stop
It seems that I need to generate diala.pdb first using diala.psf file and
initial embedding of coordinates, but I can't find any place in manual or
on-line how to do this.
Could you please help me to generate .pdb by initial embedding of
coordinates into .psf file.
Thank you very much for all your help!!
--
Best regards,
Anna Kuznetsova
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