AMBER Archive (2008)

Subject: Re: AMBER: trajout input

From: Swarup Gupta (swarupgupta_at_yahoo.com)
Date: Sun Jun 22 2008 - 22:01:31 CDT

Hi Thomas,
 
You can also use ptraj to write a new trajectory for the set of atoms of your interest. e.g. If you have a trajectory of protein, ligand, water and ions and if you want to have a trajectory of only protein (say protein.trj) then in your ptraj script you can strip out ligand, water and ions. Follow the similar procedure to get the trajectory of the ligand. 
 
You had a second query:
"Will the same prmtop can be used for the PCA analysis?"
 
The answer is the prmtop will have to be compatible with the trajectory you are giving as input. So if if you are using "protein.trj" for your input you would need the corresponding "protein.prmtop". This is not only for PCA but it is generally true for all analyses.
 
 
regards,
SG

--- On Fri, 6/20/08, Thomas Leonard <thomasj_at_bii.a-star.edu.sg> wrote:

From: Thomas Leonard <thomasj_at_bii.a-star.edu.sg>
Subject: Re: AMBER: trajout input
To: amber_at_scripps.edu
Date: Friday, June 20, 2008, 5:05 AM

Hi,
Thank you,
Will the same prmtop can be used for the PCA analysis?
if so,
 how can it be?

Thomas

> Hello,
>
> MMPBSA will do that easily, but you need three prmtop files:
> - complex
> - protein alone
> - ligand alone
> See the MMPBSA manual for the script.
>
> Hope this will help
> Regards
>
> On Fri, 20 Jun 2008 17:23:55 +0800 (SGT)
> "Thomas Leonard" <thomasj_at_bii.a-star.edu.sg> wrote:
>> I have a trajectory of complex. I would like to separate the
>>receptor and
>> ligand from this. How to do this.
>>
>>
>>
>> Any help will be appreciated
>>
>>
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