AMBER Archive (2009)

Subject: Re: [AMBER] How to build reference coordinate file for targeted MD

From: gmail (heptoking_at_gmail.com)
Date: Thu Feb 05 2009 - 23:20:59 CST

Dear Dr. Simmerling
     Thank you for your suggestions. But I still did not figure out how to mannually adjust the buffer
size in order to match the water molecules in starting coordinate.I used solvateoct command and carefully
adjust the buffer size, but as my protein is quite big and surrounded by thousands of waters. I find it
quite difficult to adjust to the exact number of waters.
      Is that a way that can mannually revise the topology or the coordinate file? I do not know the
exact organization format of inpcrd file so no clue for this.


Thank you!

Xiaonan


 

--------------------------------------------------
From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
Sent: Thursday, February 05, 2009 7:19 PM
To: "AMBER Mailing List" <amber_at_ambermd.org>
Subject: Re: [AMBER] How to build reference coordinate file for targeted MD

> if they are the same protein sequence but different atom order in side
> each residue, leap will fix that.
> for the water molecules you might need to manually adjust the buffer
> size until you get the number from before.
>
>
>
>
> On Thu, Feb 5, 2009 at 1:44 AM, gmail <heptoking_at_gmail.com> wrote:
>> Dear All
>> I am trying to do a targeted MD for a big protein. There is a question on how to build a reference
>> coordinate file. As the manual pointed out that the reference coordinate are expected to match the prmtop
>> file of the starting structure. However, the starting and final structures are two different pdb files,
>> which although have the same amino acid sequence, the exact atom sequence are somewhat different. In addition,
>> I am thinking that if I create the solvated reference prmtop and inpcrd files, the number of water molecules
>> will be slightly different to those generated with starting pdb file. That will most probably cause failure of
>> recognition.
>>
>>
>> With no definite solution in my mind, I have to ask experts for suggestions.
>>
>>
>> Thank you in advance.
>>
>>
>> Cheers!
>>
>>
>> Xiaonan Zhang
>>
>> Shanghai public health clinical center
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>
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