Dear Amber users,
I have .prmtop and .inpcrd files for a dimer unit which is one lattice unit
that makes up an ordered assembly. I would like to make input files for the
whole assembly (x60 of the dimer unit). So I have one prmtop file that
describes all interactions (dimer.prmtop) and several coordinate files. To
do this, just to test the principle, I have first tried using addles to
generate the input files for a pair of dimer units. So I try a script
addles.in:
file rprm name=(dimer.prmtop) read
file ucrcd name=(dimer.inpcrd) pack 2 read
file wprm name (neb.prmtop) wovr
file uwcrd name(neb.inpcrd) wovr
action
omas
space numc=2 #prt 1 224 done
*EOD
addles < addles.in > addles.out
But the inpcrd file is not read or re-written and I get the following error
in addles.out:
'Warning-old coordinate file not specified'
'New Coordinate file will not be created'
The .prmtop file is written but not the .inpcrd file. If I create the
neb.inpcrd by hand and view neb.prmtop and neb.inpcrd in VMD the atom
assignments are all wrong for the 2 dimer units.
If I follow the instructions in the 'nudged elastic band' tutorial:
http://ambermd.org/tutorials/advanced/tutorial5_amber9/section3.htm
I also get similar issues (the .prmtop file is generated ok, but not the
.inpcrd). Please does anybody see what the problem may be?
With thanks,
Jenny
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Received on Mon Nov 07 2011 - 09:30:05 PST
