AMBER Archive (2005)

Subject: Re: AMBER: some problems with Antechamber

From: Wei Zhang (zweig_at_scripps.edu)
Date: Tue Nov 29 2005 - 11:14:53 CST

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_at_scripps.edu>
The Scripps Research Institute

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu