AMBER Archive (2005)

Subject: Re: Re: AMBER: how to reduce box size and delete excess solvent

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Wed Jul 27 2005 - 08:36:40 CDT

Dear Bill Ross,

        Thank you for your kind suggestions. But I have a system of more than 150,000 atoms. If I convert the crd file to pdb, delete the excess atoms and reload pdb file to xleap, errors are met as

======= 2005-05-15 12:50:00 you wrote£º=======

>> I would like to reduce the size of the bounding box (periodic BC) and
>> delete all solvents which don't fit inside new box. How to achieve it?
>> Can anyone furnish a script?
>
>You could use 'awk'.. something like
>
> awk '$7 < 21.4 && $8 < 30.4 && $9 < 28.2' in.pdb > out.pdb
>
>Read up on awk or perl.. some solvent molecules would
>be partial and the atoms could be replaced by leap in
>places that could lead to steric problems. The solution
>would be either a more complex script or iterative manual
>deoletion of the problem residues.
>
>Bill
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= = = = = = = = = = = = = = = = = = = =
                        
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Hanjun Zou
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel£º +86-21-50806600-1201
E-mail: hjzou_at_mail.shcnc.ac.cn
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