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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Received on Wed Apr 08 2015 - 10:30:03 PDT
