[gmx-users] Capping residues

[Sai Pooja]

I am sorry if I did not frame the question correctly, but putting it very
simply, is there a way to use capping residues with the charmm forcefield if
the residues are --COCH3 and NHCH3?

On Thu, Jul 1, 2010 at 4:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Pooja wrote:
>
>> Would it be possible to add some capping residues (like --COCH3 and
>> --NHCH3) by writing a separate .itp file and including it in the topology
>> file? Is there a way to make it consistent with charmm forcefield?
>>
>>
> No, because you have to specify bonds between these capping residues and
> your protein.  If you're #including them as new [moleculetypes], then you
> can't add these bonds.
>
>
>  Can this be done alternatively by modifying the .rtp file? If yes, what
>> other operations must one do before using these .rtp files?
>>
>>
> Reading in the manual about the file format?  I don't understand your
> question entirely.  All the other force fields use .rtp entries for caps, so
> I don't see why this couldn't be done.
>
> -Justin
>
>
> --
> ========================================
>
> 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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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