You should be able to center your 4 molecules and reimage all of your
solvent around them, in which case your won't have to worry about
imaging artifacts when using the hbond command. That assumes your box
is large enough so that there is a decent amount of clearance between
the molecules of interest and the box edge.
-Dan
On Thu, Oct 27, 2011 at 11:39 AM, mirage . <m.o.m.live.fr> wrote:
>
> Thank's,
> I am studying the complexation of four molecules (host:guest) in a solvated system. I want to count the number of hydrogen bond versus time (inter, intra and with water of my four molecule) using VMD. As water molecules are outside of the primary box, I thought it necessary to do reimage.
>
>> Date: Thu, 27 Oct 2011 10:15:47 -0400
>> From: daniel.r.roe.gmail.com
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] molecule out box and correct hbond analysis
>>
>> Hi,
>>
>> Currently the hbond routine does not use imaging. Ideally you would
>> use the center and imaging commands to reorient your molecules of
>> interest so that imaging is not a factor prior to using the hbond
>> command. Can you please post a little more information about your
>> system and how you tried to re-image it?
>>
>> -Dan
>>
>> On Thu, Oct 27, 2011 at 4:27 AM, mirage . <m.o.m.live.fr> wrote:
>> >
>> >
>> > Hi Amber users,
>> >
>> > i am using different option to reimag my molecules but in some case a part of one molecule is out box ? How to do a correct hbound analysis in this caseThanks
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Postdoctoral Associate
>> BioMaPS Institute, Rutgers University
>> 610 Taylor Road
>> Piscataway, NJ 08854
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Thu Oct 27 2011 - 09:30:04 PDT
