Dear Jiomm,
I looked at the command you used/reported:
a = sequence {a c}
Does this command make sense ?
I would use:
a = sequence {b c}
regards, Francois
> 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
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Received on Sat Feb 13 2010 - 01:00:03 PST
