Wei,
Thanks for the fast response. I'm using parmchk -i FRH.mol2 -o
FRH.frcmod -f mol2.
Normally it works fine for all of the other molecules I've done.
Really weird. Maybe there is something wrong with our particular
compilation of parmchk and I should recompile or something. It doesn't
make any sense to me...
I just checked and tleap loads it OK. So in principle I could just use
the frcmod you just sent and run that through tleap. But it hardly
seems satisfactory.
I am using a local build on a regular 32 bit intel x86 running fedora core 4.
Let me know if you have any brilliant ideas. As I said, parmchk
normally works fine (I use it all the time), so I dunno why it's seg
faulting on my machine with this particularly mol2 file but not on
yours...
Thanks
David
On 11/29/05, Wei Zhang <zweig.scripps.edu> wrote:
> Hi,
>
> parmchk can run on this molecule on my machine without a problem, the
> following is generated frcmod,
>
> -----frcmod.frh-----------------------------------------------------
> remark goes here
> MASS
>
> BOND
>
> ANGLE
> c -c3-nh 67.069 109.410 Calculated with empirical approach
> os-cc-c 70.500 119.310 same as c2-cc-os
>
> DIHE
> cd-cd-ca-ca 1 2.550 180.000 2.000 same as X -
> c2-ca-X
> nc-cd-ca-ca 1 2.550 180.000 2.000 same as X -
> c2-ca-X
> c3-cc-os-cc 1 1.050 180.000 2.000 same as X -
> c2-os-X
> cc-os-cc-cd 1 1.050 180.000 2.000 same as X -
> c2-os-X
> cc-os-cc-c 1 1.050 180.000 2.000 same as X -
> c2-os-X
>
> IMPROPER
>
> NONBON
> ---------------------------------------------------------------------
>
> what is the command you used to generate frcmod?
>
>
>
> On Tue, 2005-11-29 at 08:39 -0800, David Mobley wrote:
> > Dear all,
> >
> > I'm trying to set up a small molecule in antechamber. I begin with a
> > mdl mol file and run it through antechamber to generate bcc charges
> > and turn it into a mol2 file, then run parmchk on it. I get a
> > segmentation fault when I run parmchk. I'm attaching the mol2 file;
> > can anyone help me out? There's no error/warning message at any point,
> > so it's (obviously) rather hard to troubleshoot.
> >
> > Thanks,
> > David
> --
> Wei Zhang <zweig.scripps.edu>
> The Scripps Research Institute
>
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Received on Tue Nov 29 2005 - 19:53:01 PST
