Hello,
I have been working to convert vmd-prepared psf/crd (version 1.9.1) files
to amber-compatible formats using chamber (Ambertools 13) . The conversion
unfortunately
fails with a Fortran runtime error (bad value during integer read). The
code apparently fails during the reading of bond information, as far as I
can
tell from the psfprm.F90 file. I don't see any obvious differences in the
formatting between a working psf file and my psf file unfortunately. Note: I
adjusted the headers and formatting to reflect the 'extended' native psf (I
hope).
chamber -nocmap -top top_all36_lipid_water_ions.rtf -param
par_all36_lipid_water_ions.prm -psf XXX.out.psf -crd parv.pdb -p
test.prmtop -inpcrd
test.inpcrd -box 77.548000335693356 79.829998016357425 65.856998443603514
Any help with this problem would be very appreciated.
I have archived my input files at
https://www.dropbox.com/s/kpx1n7fzcj1871x/files.tgz
Pete
--
======================
Peter Kekenes-Huskey, Ph.D.
Postdoctoral Researcher
UCSD Dept of Pharmacology
4205 Urey Hall
9500 Gilman Avenue
La Jolla, CA 92093
http://mccammon.ucsd.edu/~huskeypm/
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Received on Mon Mar 24 2014 - 12:00:03 PDT
