On Tue, 7 Mar 2017 15:01:07 +0000
Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> If suppose I have a peptide, 5 residues long and I want to mutate
> residues 3 and 4. Is tiMerge : 1-5 :6-10 :3,4 :8,9 the right way to
> have both the mutations at a time? ________________________________
> From: Sowmya Indrakumar Sent: Tuesday, March 07, 2017 3:55 PM
> To: amber.ambermd.org
> Subject: how to use TImerge to do TI simulations
>
> Dear All,
> I am new to doing TI simulations. I know how to insert a single
> mutation (as described in the AMBER manual:
> http://ambermd.org/doc12/Amber16.pdf page 405). I was wondering if I
> can have two mutations? Is it possible to generate *parm7 and *.rst7
> for a single mutation and further use that to have the second
> mutation?
It's not entirely clear what you want to achieve. The timerge command
you suggested above is good for a mutation of two residues into two
other residues in one go. That is, the pair 3-4 can be mutated to 8-9
because timerge makes sure that residue 8 is connected to residue 2 and
residue 9 to residue 5 while residues 6, 7 and 10 are deleted.
Cheers,
Hannes.
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Received on Tue Mar 07 2017 - 07:30:03 PST
