Re: [AMBER] P450 ff from Rydberg et al.

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 08 Jun 2010 14:29:39 -0400

I think Dave is correct here.

What I think happened is that you did not explicitly added a bond when
you built the prmtp/crd in leap.

You need to look at the BOND command in the manual.

Adrian


On 6/8/10 2:25 PM, case wrote:
> On Tue, Jun 08, 2010, Renata KWIECIEN wrote:
>>
>> Since the beginning of the simulation I observe elongation of the distance
>> between iron (heme) and sulfur (CYS, axial ligand of heme) from 2.34 A in
>> the X-ray structure to 3.25 A average over 2ns production run. This
>> elongation is systematic, just in one case the distance was longer 5.1 A
>> averaged over 2 ns production run.
>
> Is there a bond between iron and sulfur? If there is supposed to be one, are
> you sure it is present in your simulations?
>
> ....dac
>
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Tue Jun 08 2010 - 11:30:07 PDT
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