Matthias Schmidt wrote:
Hi,
genbox can now modify the topology file by using genbox ... -p topol.top.
This still only works for SOL entries, as of the latest release-4-5-patches. It
would be quite useful if the topology could be updated for any arbitrary
solvent, but at present, is still limited.
-Justin
Best,
Matthias Schmidt
On Friday, August 5, 2011, lina <[email protected]
<mailto:[email protected]>> wrote:
> On Fri, Aug 5, 2011 at 7:23 PM, Ravi Kumar Venkatraman
> <[email protected]
<mailto:[email protected]>> wrote:
>> Dear all,
>> I have generated .gro and .top file for Chloranil from
prodrg
>> and tried solvate it using p
re-equilibrated cyclohexane. When i tried to
>> generate the box containing solute it is not modifying the .top file
and it
>> shows zero solvent.
>> Please help me how to solvate organic molecules that are obtainde from
>> prodrg.
>>
>> Thank you.
>
>
> Try:
>
> genbox -cp chloranil.gro -cs cyclohexane.gro -o system.gro
>
>
> and manually modify the topol.top later.
>
> you may use the solvated pre-equilibrated cyclohexane as
> cyclohexane.gro, so no need add water later.
>
> It should be no problem.
>>
>> --
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>
>
>
> --
> Best Regards,
>
> lina
> --
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--
Best,
Matthias
--
Structural Bioinformatics and Computational Biochemistry Unit
Dept. of Biochemistry
University of Oxford
http://sbcb.bioch.ox.ac.uk/schmidt.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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