Re: Protein-ligand simulation

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Jun 24 2013 - 13:15:51 CDT

Chris, thanks you! I'll be very thankful for your tutorial!

By the way what is the current most useful way to obtain charm parameters
for small ligand-like compounds (starting from its full atomic pdbs with
hydrogens) ?
With Gromacs (using charm36 force field) typically I use swiss-param server
which also produce PRM files in addition to the gromacs topology.

James

2013/6/24 Chris Chipot <chipot_at_ks.uiuc.edu>

> James,
>
> a NAMD tutorial for protein-ligand standard binding constant calculations
> is currently in alpha-version. It will be tested thoroughly in the coming
> days.
>
> If you can wait a little, I should be able to send you a copy by the end of
> this week.
>
> Chris Chipot
>
>
>
> On 6/24/13 8:51 AM, James Starlight wrote:
>
>> Dear Namd users!
>>
>>
>> I'd like to perform simulation of the protein-ligand complex ( In that
>> case I'll deal with the water-soluble diffusional ligand). Could you
>> provide me with some tutorial for such simulation ? ( in particular I'm
>> looking for additional parameters which i should specify in the conf files).
>>
>>
>> Thanks for help,
>>
>>
>> James
>>
>
>
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