[gmx-users] Unstable Minimizations
tsjerkw at gmail.com
Fri Jan 15 10:07:42 CET 2010
Okay, they're read in some cases. But not in pdb2gmx related to
building a topology as far as I can see. I should've written:
pdb2gmx doesn't distinguish between ATOM and HETATM entries.
pdb2gmx does not read CONECT records.
Now the 'TER' recoord... That makes a difference.
On Thu, Jan 14, 2010 at 9:23 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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
>> 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.
>> Tsjerk A. Wassenaar, Ph.D.
>> Computational Chemist
>> Medicinal Chemist
> 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
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Tsjerk A. Wassenaar, Ph.D.
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