Hi All,
Based on the suggestion by Jason, the following bond command has worked and
I am able to see the bond between Fe and S after loading the prmtop and
inpcrd file in vmd.
It looks like the files are ready for simulation. :)
bond P450.419.SG P450.477.FE
Thank you all.
Cheers.
Vaibhav
On Wed, Apr 8, 2015 at 6:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Apr 8, 2015 at 1:06 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> >
> >
> > On Wed, Apr 8, 2015 at 11:33 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> >
> >> Hi All,
> >> I have followed the procedure suggested and used the following modified
> >> leap input file and it seems to work except for the fact that bond
> between
> >> S and Fe is not formed.
> >> Can you please suggest on the correct usage for "bond" command? I have
> >> tried "bond P450.6768.SG P450.7755.FE 1", "bond 6768 7755 1" but got
> the
> >>
> >
> > The second number should be the *residue* number, not the atom number.
> >
>
> Sorry, I'll clarify:
>
> P450.6768.SG
>
> The above means look at the 6768th residue of the P450 unit (which you
> defined via loadPDB), and take the atom named SG from the residue you
> selected (the 6768th residue).
>
> The second proposed syntax: "bond 6768 7755 1" is wrong. tleap doesn't
> know that "6768" or "7755" are atom numbers... or what system they would
> correspond to, anyway.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Apr 09 2015 - 02:30:03 PDT
