AMBER Archive (2008)

Subject: Re: AMBER: how to overcome theunusual bonds formation

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu May 29 2008 - 07:07:14 CDT

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
>>
>> --
>> -------------------------------------------------------------------------------
>> Florian Haberl
>> Computer-Chemie-Centrum
>> Universitaet Erlangen/ Nuernberg
>> Naegelsbachstr 25
>> D-91052 Erlangen
>> Telephone: +49(0) − 9131 − 85 26573
>> Mailto: florian.haberl AT chemie.uni-erlangen.de
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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

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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