[gmx-users] Topology from semiempiricaly optimized structure

[Yiannis]

Hello,
from my experience the best think to do in your case would be to  
generate an entry in the ff*.rtp file (* stands for your force field of  
choice) and then use pdb2gmx to generate your topolgy. After what you  
edit the topology at your needs.
But first you have to look at the ff*.atp file and assign atom types to  
your atoms.
Ioannis

Le lundi, 14 jun 2004, à 08:44 Europe/Paris, Semen Esilevsky a écrit :

> Dear Daan van Aalten,
> The problem is that I already have the optimized
> geometry, so thre is no need to "guess" it. What I
> need is just to generate all the topology entries and
> assign the force constants to them, but the
> equilibrium values of bond length and angles have to
> remain the same as in the input structure. Imho, if
> PRODRG had such a feature is would be even more
> usefull for people.
>
> --- Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
> wrote:
>>
>> Hi Semen
>>
>> Would it be possible for you to send us the input
>> coordinates so we can
>> see what goes wrong? Do I correctly interpret your
>> E-mail to say that the
>> coordinates are screwed up even if you minimize on
>> the server?
>>
>> cheers
>>
>> Daan
>>
>> On Sat, 12 Jun 2004, Semen Esilevsky wrote:
>>
>>> You see, I've tried PRODRG and it does not work
>> for
>>> me. It disrupts the geometry I supply even if I
>> don't
>>> ask for energy minimization. I'm not sure if it is
>> a
>>> bug, but this server doesn't help much.
>>>
>>> --- Daan van Aalten
>> <vdava at davapc1.bioch.dundee.ac.uk>
>>> 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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>>
> ####################################################################### 
> #######
>>>> Dr. Daan van Aalten                    Wellcome
>>>> Trust Senior Fellow / Reader
>>>> Wellcome Trust Biocentre, Dow Street   TEL: ++
>> 44
>>>> 1382 344979
>>>> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++
>> 44
>>>> 1382 345764
>>>> School of Life Sciences                E-mail:
>> see
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>> Dr. Daan van Aalten                    Wellcome
>> Trust Senior Fellow / Reader
>> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44
>> 1382 344979
>> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44
>> 1382 345764
>> School of Life Sciences                E-mail: see
>> WWW page
>> Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
>> http://davapc1.bioch.dundee.ac.uk
>>
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