Tsjerk Wassenaar skrev:
Hi Jack,
On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz
<[email protected] <mailto:[email protected]>> 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
[email protected] http://xray.bmc.uu.se/molbiophys
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