AMBER Archive (2009)

Subject: Re: [AMBER] Load protein complex to Xleap (Combine)

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sat Mar 28 2009 - 20:17:21 CDT

Dear Dr. David,
 
Thanks for your reply! I believe my problem can be solved now!
 
You ever asked me why I want to load the org. and receptor separately. The reason is as follows:
I ever came across a problem-when I docked small peptideswith anmino acid residues aranged between 12_20. You know, when I docked them in to the protein in sybyl, I found these peptides were not considered to be usual amino acid any more. So I have to load those small peptide in the mol2 form. But you know, these are peptides rather than small organic molecules! This means, I could not use the antechamber to produce the prepin and frcmod file to load those mol2 molecules to produce the promtop and inpcrd in xleap. Because, the atoms in these peptides  outweigh the MAX of the memory.
 
So now, I want to divided these pepetides(mol2) into small segments(mol2). And then use the antechamber to produce the prepin and frcmod files of the segments. When all the segments of a peptide were produced, I then load them into the xleap to produce an intact peptide again! But you know, these segment will not be contacted with each other, so I just need to link them and do some revision, such as atom type and charge to those atoms.
 
Finally, do you think wheather I can obtain the the preppin and frcmod files of the whole small peptide or not? Do you think this way is feasible or not? Do you have better approaches?
 
I am really eargerly hoping  you can give me some help! Because ,you know this is a very typical problem.
 
Best wishes
 
Rilei Yu

9日，周日, David A. Case <case_at_biomaps.rutgers.edu> 写道：

发件人: David A. Case <case_at_biomaps.rutgers.edu>
主题: Re: [AMBER] Load protein complex to Xleap (Combine)
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年3月29日,周日,上午5:39

-----下面为附件内容-----

On Sat, Mar 28, 2009, Rilei Yu wrote:
>  
> I want to perform MD on my protein complex which consits an organic
> molecue and a receptor. As there is no field paremeters for this organic
> molecue, I used ANTECHAMBER to obtain the org.prepin and org.frcmod
> files. Then I obtained the ptomtop and inpcrd successfully, but I still
> have some problems. After load org and receptor to xleap I find the org
> (Ligand) was not in the binding cavity.

This is to be expected: the coordinates in the prep file are not those
from the complex.

> (I can load the complex accurately by loading  the procomplex directly,
> but now I want to load the receptor and ligand respectively!)

It's not clear why you want to load the two separately.  But if you do,
edit the complex file to create separate pdb files (receptor and ligand),
then use two loadpdb commands to bring both into leap -- that way you will
get the coordinates of the complex for both.

...dac

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