AMBER Archive (2005)

Subject: AMBER: question about xwin load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Fri Jan 28 2005 - 10:48:28 CST

Dear Ross,

Since my nuc.pdb file cannot be opened by x-win, I have downloaded the nuc.pdb
file and nuc_ter.pdb from the tutoral website. The result is same. I edit DA5,
x-win32 also do nothing on the screen. Edit LYS gives me same result with
aboves.
Before amber8 was installed, we have downloaded all of bug fix files from
amber's website.

Here is the pdb file and leap test .log file.

Thanks!

Xiaowen

> Dear Xiaowen
>
> > I installed AMBER8 on unix and installed X-win32 on windows
> > computer. By using
> > x-windows terminal,
>
> I use this type of setup all the time so it shouldn't cause you and
> problems.
>
> >I follow everything from the tutorial 1
> > to 3 to generate
> > nuc.pdb, loadpdb and so on.
> >
> > $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> > so far, everything is fine, same as the tutorial showed us.
> >
> > dna1=loadpdb "nuc.pdb"
> >
> > message as following:
> > ============================================================
> > dna1=loadpdb "nuc.pdb"
> > (starting new molecule for chain T)
> > --residue 536870912: duplicate [] atoms (total 438)
>
> This is a very strange error. It suggests a corrupted pdb file. Can you post
> me the nuc.pdb file that you are trying to load and I'll take a look. Also
> download the pdb from the link on the tutorial page and compare it to the
> one you made by following the steps in the tutorial. They should be
> identical.
>
> > edit dna1
> >
> > graphic window come out but did nothing. no graphy.
> > Is the problem from my installation or from This X-windows,
> > or others, like
> > unix computer's memory (now it is 1 Gb)?
>
> This is almost certainly a problem with the pdb file. Try running xleap as
> stated in the tutorial and type edit LYS - it should come up showing you a
> lysine residue.
>
> > Then,
> > I go to the $AMBERHOME/test/make test
> >
> > stop in
> > cd qmmm/standard; ./Run.lysine
> > =================================================
> > exec():0509-036 cannot load program ../../../exe/sander.QMMM
> > because of the
> > following errors: 0509-026 system error: there is not enough
> > memory available
> > now.
> > ./Run.lysine: Program error
> > make: 1254-004 the error code from the last command is 1.
>
> I take it all the tests before this passed. If they did then I wouldn't
> worry about this test. You won't need sander.QMMM unless you want to run
> QMMM calculations. You need to apply the bug fixes before you can use this.
> You also need to increase the limits in your shell using the ulimit command.
> For the moment I wouldn't worry about it.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

xiaowen

Chemistry Department
Iowa State University
Office phone number: 515-294-4285


  • chemical/x-pdb attachment: nuc.pdb

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu