AMBER Archive (2006)

Subject: Re: AMBER: Trouble with Leap

From: Biswa Ranjan Meher (brmeher_at_iitg.ernet.in)
Date: Thu Oct 19 2006 - 00:28:46 CDT

Dear Amber Users,

I am doing FEP calculation for a protein system in an aqueous solution. I
want to mutate some of the residues in the protein. For this I loaded the
protein in xleap , selected all the atoms and through edit selected atoms
from the unit editor menu bar created the spreadsheet editor to edit the
residues of the protein.But strange thing is that in the spread sheet
editor (editor table) I got the lists of atoms of FEW residues but NOT
ALL. I hope this problem is with the large protein system with aqueous
solution. As I removed most of the water molecules from the protein, it is
being possible to edit all the aminoacid residues with all the atoms
in the editor sheet. But I want to edit the protein in presence of all the
water molecules in the protein system.

I mailed this problem in my previous mail and got one reply to do the same
job in LEaP command line. But I am not being able to give the appropriate
command in the LEaP command line for the said problem. So can anybody
please suggest how exactly I have to do this and what commands I have to
follow in the LEaP command line to solve this problem.

Thanks for your suggestions in advance.

regards
B. R. Meher --

On Wed, 18 Oct 2006, Biswa Ranjan Meher wrote:

> Dear Dr Scott,
>
> Thank you for your suggestion. But one thing I am getting problem is that my
> protein is a large one and in an aqueous solution. While editng the protein
> along with water I am not getting all the residues in spreadsheet editor, but
> when I removed most of the water molecules from the protein system, it is
> being possible to edit all the aminoacid residues with all the atoms in the
> editor sheet.
>
> As you have suggested in your previous mail, "anything that can be done in
> the editor can be done with the LEaP command line (as far as I know)". But
> can you please suggest me how exactly I have to do this in the LEaP command
> line.
>
> with regards
>
> B. R. Meher
>
>
>
>
>
>
> On Mon, 9 Oct 2006, Scott Brozell wrote:
>
>> Hi,
>>
>> On Mon, 9 Oct 2006, Biswa Ranjan Meher wrote:
>>
>>>
>>> Dear Amber users
>>> I am having trouble with Leap. The problem is that I want to edit one
>>> protein in xleap. I loaded one pdb file in xleap and by edit selected
>>> atoms from the menu bar selected all the atoms of the protein. But strange
>>> thing is that in the spread sheet editor (editor table) I got the
>>> lists of atoms of FEW residues but NOT ALL. So my querry here is that, is
>>> there any
>>> tricks, which I am missing here to visualize all the atoms of all the
>>> residues of the protein concern in the spread sheet editor?
>>>
>>> I am running xleap on a Linux (redhat 8.0) system.
>>>
>>> Has anyone else run into this problem and knows how to correct it?
>>
>> No. For example, I loaded 228 residue 1E1J, edited that unit,
>> and can scroll down to what seems to be the last residue.
>> I note that it takes a couple of seconds for the table contents to
>> catch up to rapid scrolling and that the end of the scroll extends
>> past the end of the contents of the table.
>> But I do not see any obvious failure.
>> You'll need to provide a detailed example to reproduce any problems
>> that you have.
>>
>>> From a different perspective, why would one want to edit a big protein
>> this way ? Anything that can be done in the editor can be done with
>> the LEaP command line (as far as I know).
>>
>> HEADER PRION PROTEIN 08-MAY-00 1E1J
>>
>> Scott
>>
>>
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>
> 

-- 
......................XXXXXXXXXXXXXXXXXX................................
Mr. Biswa ranjan Meher (Research Scholar)          Room:119
Dept. Of Biotechnology, IIT-Guwahati,              Siang Hostel
North Guwahati, Assam-781039                       IIT-Guwahati
Phone:0361-2582246(Lab)                            Phone:0361-2582766/7/8
...........................................
Mob:+919435014189,
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