AMBER Archive (2005)

Subject: Re: AMBER: Bromelain PDF xleap load error (Proton Problems?)

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Thu May 05 2005 - 19:37:36 CDT

Dear Patko:

You can use the simple unix/linux "grep" command to strip your protons in
PDB.

grep -v '^.............H' old.pdb > new.pdb

There are totally 13 dot in this command which means the line with the
fourteenth character of H will be omitted.

Regards!

Liu

On Fri, 06 May 2005 06:02:40 +0800, Thomas Patko <tpatko_at_csulb.edu> wrote:

>
> AMBER Users:
>
> After looking at the input PDB with a graphical viewer (PCModel9) it
> seems that the problem may be related to stray or misplaced protons in
> the PDB. I have not been able to find the command to strip all protons
> from my original PDB. There are also missing parameters when trying to
> do a minimization in PCModel on this original PDB using the built-in
> AMBER forcefield (segmentation faults results). I know that I can
> reprotonate with the command line protonate program once I have stripped
> the erroneous or stray protons out.
>
> Any helps would be appreciated.
>
> Regards,
>
> Thomas Patko
>
> Graduate Student
> Department of Chemistry & Biochemistry
> California State University, Long Beach
> Dr. Marco Lopez Research Group
>
> On Wed, 04 May 2005 10:13:35 -0700
> "Thomas Patko" <tpatko_at_csulb.edu> wrote:
>> AMBER Users:
>> I am trying to load the very small protein bromelain to do some MD
>> simulations. There seems to be a problem with the connectivity between
>> each residue when I load it in xleap. Am I doing something wrong here
>> or is there a problem with the initial PDB file? The protein of
>> interest is attached to this e-mail as is my output from xleap
>> (leap.log) when I try to load the protein in xleap.
>> Regards,
>> Thomas Patko
>> --
>> Graduate Student
>> Department of Chemistry & Biochemistry
>> California State University, Long Beach
>> Dr. Marco Lopez Research Group
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-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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