Hi Thomas,
It seems to me that you are talking about something which you see during visualization, but you do not get any such message during minimization.
If so then load your topology first in VMD and then load the coordinate/trajectory. Hopefully you will see the correct bonds.
regards,
SG
Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
By bond formation you mean when visualized ? Please let us know what do
you mean by a bond forming during minimization.
If so, are you loading your prmtop file into whatever program you use
for visualization or are you using a pdb file ?
Most visualizers (e.g. VMD), when given a pdb file, will decide on the
bonding pattern on their own, based on pure distances.
As Florian mentioned, classical MD in amber only has the bonds YOU
created initially, not more, not less. So, they can never just 'appear'.
Adrian
Thomas Leonard wrote:
> Hi,
>
> Thanks for your reply,
> But even during the minimization (before MD) itself unusual bond formation
> occurs in those specific nitogen carbon and oxygen.
>
> Thomas
>
>
>> Hi,
>>
>> On Thursday, 29. May 2008 13:03, Thomas Leonard wrote:
>>> Hi,
>>>
>>> Why unusual bonds are formed during minimization.
>>>
>>> In my case I have problem with unusual bond formation (which is not
>>> expected) at the nitrogen,oxygen of FADH cofactor
>> in normal MD simulation no bond breaking can occur.
>>
>> Your question is not clear to me, I think you have done following:
>>
>> If you calculate an average structure of your simulation and than view it
>> as a
>> pdb file, than you can see "unphysical bonds".
>> Easy solution is to minimize this average structure.
>>
>>
>>> Thomas
>>>
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>> Greetings,
>>
>> Florian
>>
>> --
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>> Florian Haberl
>> Computer-Chemie-Centrum
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>
>
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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
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Received on Sun Jun 01 2008 - 06:07:30 PDT
