Can you post two snapshots before and afer here?
Hai
On Tue, Feb 14, 2017 at 12:42 PM Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:
> Dear David,I have used following command for re-imaging trajectories;parm
> complex.prmtoptrajin md_simulation1.mdcrd.gztrajin ...trajin ....trajin
> ....trajin ....trajin .....trajin .......trajin md_simulation50.mdcrd.gz
> strip :NA+,WAT outprefix nowatertrajout reimaged-complex.mdcrd
> In original script I have pasted trajin from md_simulation1.mdcrd.gz and
> so on but here I used dots just to shrink my script. Please help me to
> resolve this issue.
> Thanks Best Regards, Saman Yousuf Ali
>
> On Tuesday, February 14, 2017 9:15 AM, David Case <
> david.case.rutgers.edu> wrote:
>
>
> On Tue, Feb 14, 2017, Saman Yousuf ali wrote:
>
> > I have also visualized
> > trajectories before and after re-imaging using vmd. In both cases, after
> > few frames one monomer move away from another. Both chains are not
> > bonded with each other but are very close. I am unable to understand
> > this issue. You told me that I should specify anchor molecule for
> > re-imaging. My target system consists of chain A 1-267 residues, chain B
> > 268-354 residues, co-factor and ligand of chain A 355-356, and co-factor
> > and ligand of chain B 357-358 molecules. Can you please suggest me
> > anchor molecule for my case.
>
> Sounds like you should image only the solvent, keeping both chains and both
> ligands fixed. Others on the list are probably more experienced in this
> and
> may have better suggestions.
>
> If things don't work, be sure to post the exact commands you gave to
> cpptraj:
> there is often an important distinction between what you intended to do,
> and
> what you actually did.
>
> ....dac
>
>
>
>
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Received on Tue Feb 14 2017 - 10:30:03 PST
