[gmx-users] Unstable Minimizations

[Erik Marklund]

Tsjerk Wassenaar skrev:
> Hi Jack,
>
> On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz 
> <js at drugdiscoveryathome.com <mailto: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.
I may be wrong, but I think Gromacs reads CONNECT records nowadays.

/Erik
>
> Cheers,
>
> Tsjerk
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys