VMD-L Mailing List

From: Jeff Ames (ames_at_alpha.ces.cwru.edu)
Date: Wed Jul 17 2002 - 01:51:49 CDT

Hello --

I'm trying to read in a parm and crd set from AMBER 7, in VMD 1.7.1 under
Linux. But VMD seems to choke on the parm file, saying "not equipped to
read perturbation prmtop". From the code (parm.c) it seems like it's
reading the ifpert value of the parm file as being nonzero, though from
looking at the parm file, it looks like it should be 0....

The POINTERS section of my parm file is as follows (spaces adjusted so
it'll fit on a single line):

%FLAG POINTERS
%FORMAT(10I8)
   11183 17 10761 452 554 694 946 1128 0 0
   17598 3547 452 694 1128 34 59 31 27 1
       0 0 0 0 0 0 0 1 33 0
       0

I believe the first number on the third line is the ifpert value (0).
I've tried setting every number here to 0 (simultaneously), and I've
gotten the same error, so it seems that VMD is getting completely confused
about the file somewhere. It's an AMBER 7 format file, and starts off
with %VERSION. If it does determine the version correctly (anyone know
how to see the iout stream output?), then it's also doing all the
moveto()'s right, as it doesn't leave that function before the ifpert
check. So I'm not sure what's going wrong here.

I've also tried VMD 1.8a16, but it crashes when I try to open the parm/crd
files, with no output.

Any ideas? I can provide the full files I'm using if it'd help.

TIA,
Jeff