Dear Fyd and Bill Ross and AMBER developers;
thanks for reply but my problem is not solved yet.
>> Someone may need to debug leap using your input files
> who can help me ?
*******>>>>>>>>Amber developers most likely<<<<<<<<<<<<<*********************
=> I get 1000 GLY residues without any problem.
In my case its not a linear sequence, it is branched. Script (that is how to join residues) is written by some programme which is understood by tleap. But after joining number of residues it is giving error and my linux system gets hanged up. This will help me (and others) to generate macro structures in AMBER itself, without external tool
please help to sort out this error
regards and thanks;
JIomm
--- On Thu, 2/11/10, FyD <fyd.q4md-forcefieldtools.org> wrote:
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] limit of joining residues
To: "amber" <amber.ambermd.org>
Date: Thursday, February 11, 2010, 10:47 AM
Dear JIomm,
> I have joined the residues by defining head and tail atoms and sequence
> command in tleap. the system is macromolecule like. so is there any
> limit of number of residues that can be added.
If you use the "sequence" command of LEaP to create a very long peptide sequence, the conformation will be extended. If you solvate the corresponding system the box size will be quite huge...
You might try to follow a different approach. Use a builder different to LEaP to generate a PDB file that you will load in LEaP in a second step. For instance insightII under SGI can do this job. I am sure you can find other tools to do that...
Or you might try to build your peptide using a different approach in LEaP. I did a quick test:
a = sequence { GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY }
b = sequence { a a a a a a a a a a }
c = sequence { b b b b b b b b b b }
desc c
=> I get 1000 GLY residues without any problem.
did I miss something ?
regards, Francois
_______________________________________________
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
Received on Sat Feb 13 2010 - 00:30:02 PST
