[gmx-users] Unstable Minimizations

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 14 17:54:42 CET 2010

Hi Jack,

On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz <js at drugdiscoveryathome.com>wrote:

> Problem Solved.
> I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept
> TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other
> non-AminoAcid residues were present. Most of this is described by the
> FFAmber site
> http://chemistry.csulb.edu/ffamber/

Gromacs doesn't distinguish between ATOM and HETATM entries.
Gromacs does not read CONECT records.
Now the 'TER' recoord... That makes a difference.



Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100114/835db29a/attachment.html>

More information about the gromacs.org_gmx-users mailing list