AMBER Archive (2008)

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

From: Swarup Gupta (swarupgupta_at_yahoo.com)
Date: Thu May 29 2008 - 07:27:36 CDT


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_at_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
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>> 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
>> -------------------------------------------------------------------------------
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-- 
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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo_at_scripps.edu

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo_at_scripps.edu