[gmx-users] Topology from semiempiricaly optimized structure

[Erik Lindahl]

Hi,

I should probably also clarify that I wasn't referring to PRODRG when I  
talked about commercial programs that had problems generating  
topologies automatically :-)

Cheers,

Erik


On Jun 12, 2004, at 11:04 AM, Daan van Aalten wrote:

>
> if you are happy with sticking with the ffgmx force field, the PRODRG
> server will give you a topology for your molecule, see
> http://davapc1.bioch.dundee.ac.uk/prodrg
>
> Daan
>
> On Fri, 11 Jun 2004, Semen Esilevsky wrote:
>
>> Hi all!
>> I have a small molecule (a fluorescent probe), which
>> is optimized on the semiempirical level, so I know the
>> geometry. As far as I understand the only way to make
>> a topology for it is to write it by hands using
>> appropriate atom types and forcefield parameters.
>> However it seems to be a week of work for ~80 atoms.
>> Does the program (or script) exists for this routine
>> task?
>>
>> Thank you in advance,
>> Semen
>>
>>
>>
>>
>>
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>
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> #######
> Dr. Daan van Aalten                    Wellcome Trust Senior Fellow /  
> Reader
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