AMBER Archive (2004)

Subject: Re: AMBER: sander : constraints to conserve hydrogen bonds

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Jul 23 2004 - 07:08:43 CDT

I think for hydrogen bonds it would be better to use nmropt
than ntr. ntr will restrain atoms to particular Cartesian coordinates,
but nmropt will allow a distance restraint to be used for each hydrogen
bond.
check the sander manual for details on distance restraints.

Jiten wrote:

>Hello,
>
>Use ntr options - you need to define the atoms to be conserve at the end of
>the input file. There are examples on it.
>
>
>----- Original Message -----
>From: "sachin patil" <sachin_ppatil_at_yahoo.com>
>To: <amber_at_scripps.edu>
>Sent: Friday, July 23, 2004 1:15 PM
>Subject: AMBER: sander : constraints to conserve hydrogen bonds
>
>
>
>
>>Hi,
>> I am running MD simulations on a receptor-ligand
>>complex.And wish to conserve some of the hydrogen
>>bonds between the ligand and the receptor residues.
>>But I dont exactly know how do I achieve that.
>> Any help, suggestions would be highly aprpeciated !!
>>
>>Sachin Pati
>>------------
>>Dept. of Medicinal & Biological Chemistry
>>University of Toledo,Toledo
>>Ohio, 43606
>>
>>
>>
>>
>>
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