AMBER Archive (2003)

Subject: Re: AMBER: import pdb file in xleap

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Aug 07 2003 - 18:25:18 CDT

Hello,

Please submit reproducible bug reports.
This includes the platform, the MACHINE file, and the EXACT
sequence of commands executed. I cannot reproduce your problem:

For example I loaded a pdb (examples/bpti/6pti.mod.pdb) and erased
several atoms without explicitly erasing any bonds first and without
a crash; here is my report:

Amber 7 was built using Machine.ifc; ifc version 7.1 gcc version 3.1.1.
xleap was started on an Intel 2.00GHz XEON running Linux 2.4.18-5
source leaprc.ff99
p=loadpdb 6pti.mod.pdb
edit p
the protein was rescaled using the mouse
the Erase manipulation button was clicked
6 atoms were erased.

Here is the tail of leap.log
> edit p
Unit Editor: Breaking bond: .R<PHE 45>.A<CB 5> - (null)
Unit Editor: Breaking bond: .R<PHE 45>.A<CD1 9> - (null)
Unit Editor: Breaking bond: .R<PHE 45>.A<CD2 17> - (null)
Unit Editor: Breaking bond: .R<ARG 53>.A<H 2> - (null)
Unit Editor: Breaking bond: .R<ARG 53>.A<CA 3> - (null)
Unit Editor: Breaking bond: .R<MET 52>.A<C 16> - (null)
Unit Editor: Reseting connect#0 in .R<ARG 53>
Unit Editor: Breaking bond: .R<ALA 40>.A<CA 3> - (null)
Unit Editor: Breaking bond: .R<ALA 40>.A<O 10> - (null)
Unit Editor: Breaking bond: .R<LYS 41>.A<N 1> - (null)
Unit Editor: Reseting connect#1 in .R<ALA 40>
Unit Editor: Breaking bond: .R<ARG 53>.A<CA 3> - (null)
Unit Editor: Breaking bond: .R<ARG 53>.A<HB2 6> - (null)
Unit Editor: Breaking bond: .R<ARG 53>.A<HB3 7> - (null)
Unit Editor: Breaking bond: .R<ARG 53>.A<CG 8> - (null)
Unit Editor: Breaking bond: .R<GLN 31>.A<H 2> - (null)
Unit Editor: Breaking bond: .R<GLN 31>.A<CA 3> - (null)
Unit Editor: Breaking bond: .R<CYX 30>.A<C 9> - (null)
Unit Editor: Reseting connect#0 in .R<GLN 31>
Unit Editor: Breaking bond: .R<ILE 18>.A<CB 5> - (null)
Unit Editor: Breaking bond: .R<ILE 18>.A<HG12 12> - (null)
Unit Editor: Breaking bond: .R<ILE 18>.A<HG13 13> - (null)
Unit Editor: Breaking bond: .R<ILE 18>.A<CD1 14> - (null)

Please send a reproducible bug report for your problem.
Since the Amber List has message size and attachment restrictions,
give exact instructions on how to obtain the pdb file, etc.

Sincerely,

Scott Brozell, Ph.D. | e-mail: sbrozell_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-8754
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/~sbrozell

On Thu, 7 Aug 2003, Vikas Varshney wrote:

>
> Hi Mikyung..
> about your second question.. for removing atoms efficiently
> without any
> segmentation fault, first remove the bond between the atoms. Then
> remove the atom
> which has no bonds now. If you click on the atom which is bonded
> to someone,
> xleap would crash. First make sure that the atom you are going to
> delete is lone.. No
> bonds..
> Hope this would be of your help..
>
> Vikas
> On Fri, 08 Aug 2003 Mi-Kyung Seo wrote :
> >Hi Amber users,
> >
> >I have two questions about xleap. (Version: Amber 7.0)
> >
> >1. When I open pdb file which is created by Insight and edit this
> >unit (unit editor),
> the structure contatins only dots, no bonds.
> >However, everything is ok with pdb viewer (e.g.VMD)
> >xleap can't read pdb file made from Insight??
> >
> >2. I got segmentation fault and xleap is closed right away when I
> >build new
> molecule and try to remove atom in unit editor of xleap. I clicked
> "remove" button
> with mouse and picked atom which I wanted to remove.
> >
> >Thanks.
> >Regards,
> >Mikyung
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