[gmx-users] Unstable Minimizations

[Tsjerk Wassenaar]

Hi,

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.

Cheers,

Tsjerk

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
>>    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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist