Re: Chains, LEaP and ambpdb

From: Ioana Cozmuta <>
Date: Tue 17 Dec 2002 13:07:24 -0800 (PST)

Hi Luis,

I do not know another way around then writing a small C code for yourself
that does the job you want (number the water residues and atoms up to the
limit you want to).
About reading the restrt file into leap, I think that there was a similar
question a while ago and the answer was that you can only read it back if
you transform it into a pdb file. However, if you do not want to go
through the trouble of generating a pdb file back from the amber output
files (top and crd) you can try to use VMD and load the .crd file with it.
Alternatively you may want to try to use babel to transform amber files
into pdb files or SIMULAID (
-software free to download for academic use). I did not try Babel myself
on this but I've tried Simulaid and it's a nice software that works well
and has lots of useful features.

Hope this helps,

* Ioana Cozmuta, PhD * *
* NASA-AMES Research Center * "Gravitation can not be held responsible*
* Mail Stop 230-3 * for people falling in love" *
* Moffet Field,CA 94035 * *
* phone: (650) 604-0993 * Albert Einstein*
* fax: (650) 604-0350 * (1879-1955) *

On Tue, 17 Dec 2002, Luis Gracia wrote:

> Hi everybody!
> I constructed a system with LEaP that has more than 10000 waters. When
> converting the files to pdb with the program ambpdb I get **** in the
> residue number from 10000 up. Does anyone know about a script to get
> around this, may be adding chain labels every 10000 water molecules? I
> also need to read a md simulation output from this system back in LEaP
> again, and it seems to me that it is only possible converting the
> restart file to pdb. Is there a way to input the amber restrt file into
> LEaP?
> Thank a lot, and happy holidays!
> Best, Luis
> --
> Luis Gracia, PhD
> Dept. Physiology & Biophysics, 21-280
> Mt Sinai School of Medicine
> One Gustave L. Levy Place, New York NY 10029
> Tel: (212) 241-0858 --- Fax: (212) 860-3369
> e.mail:
Received on Tue Dec 17 2002 - 13:07:24 PST
Custom Search