AMBER Archive (2005)

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

From: Thomas Patko (tpatko_at_csulb.edu)
Date: Wed May 11 2005 - 02:10:53 CDT

Thank you. That worked fantastic!

Regards,

Thomas

Graduate Student
Department of Chemistry & Biochemistry
California State University, Long Beach
Dr. Marco Lopez Research Group

On Fri, 06 May 2005 12:05:36 +0100
  Andy Purkiss <a.purkiss_at_mail.cryst.bbk.ac.uk> wrote:
>
> Try the following awk command to remove hydrogens
>
> awk '($3 !~ /^[123]?H/ ){print}' pdbinputfile >
>pdbfile_nohydrogens
>
>
>
> On Thu, 2005-05-05 at 23:02, Thomas Patko 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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Graduate Student
Department of Chemistry & Biochemistry
California State University, Long Beach
Dr. Marco Lopez Research Group
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