[gmx-users] Capping residues
saipooja at gmail.com
Thu Jul 1 23:27:06 CEST 2010
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 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
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