AMBER Archive (2005)

Subject: RE: AMBER: antechamber -- missing improper torsions

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Oct 18 2005 - 22:33:13 CDT

Hi David,
 
Oh this is more complicated then. Is it possible for you to send me the
files you are using and the steps you are doing so I can reproduce it and
take a look.
 
Thanks
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David Mobley
Sent: Tuesday, October 18, 2005 12:22
To: amber_at_scripps.edu
Subject: Re: AMBER: antechamber -- missing improper torsions

Ross,

No, it isn't putting them in the frcmod file. The errors I show are in leap
when it tries to generate the prmtop file; it can't find some of the
torsions it's looking for. And I had just applied all of the bugfixes two
days before sending my original e-mail, so if it's a bug that has been
fixed, the patch should be included in my compilation of amber.

Thanks,
David

On 10/17/05, Ross Walker <ross_at_rosswalker.co.uk> wrote:

This may be a leap bug rather than an antechamber bug. Is antechamber
putting the impropers in the frcmod file but leap just not putting them in
the prmtop file?
 
If so then try applying bugfix.53 from
http://amber.scripps.edu/bugfixes80.html
 
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 <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.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David Mobley
Sent: Monday, October 17, 2005 11:34
To: amber_at_scripps.edu

Subject: AMBER: antechamber -- missing improper torsions

Dear all,

I wrote some time ago to the list because antechamber is failing to put some
of the necessary improper torsions for a small molecule I'm trying to set up
in the frcmod file it generates. Can anyone shed some light on why
antechamber is missing these, and what the fix is?

See my original e-mail below, and attached are some files you should be able
to use to reproduce the problem.

Thanks,
David

---------- Forwarded message ----------
From: David Mobley <dmobley_at_gmail.com>
Date: Sep 28, 2005 3:35 PM
Subject: AMBER: antechamber -- missing improper torsions
To: amber_at_scripps.edu

Dear all,

I'm generating AMBER parameters for a small molecule, flavin mononucleotide
(FMN) with AMBER using antechamber on the pdb file (with all hydrogens), and
antechamber is failing to put some of the required improper torsions for
this molecule in the frcmod file that parmchk generates. Any idea why? Here
are the particulars:

I use "antechamber -i (pdb file) -fi pdb -o (mol2 file) -fo mol2 -c bcc",
then run "parmchk -i (mol2 file) -f mol2 -o frcmod". I'm attaching a copy of
the pdb file, which comes from here:
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record
<http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=
CHEM_COMP&PRIMARYKEY=1569&PARENTINDEX=-1&APPLICATION=1>
&ENTITY=CHEM_COMP&PRIMARYKEY=1569&PARENTINDEX=-1&APPLICATION=1

I am using the latest version of AMBER and just applied all of the bug fixes
two days ago. The errors I get only show up in my leap.log (leap writes out
the prmtop and crd files without complaining) and are:

 ** Warning: No sp2 improper torsion term for c-ne-cd-cd
        atoms are: C4 N5 C4A C10
 ** Warning: No sp2 improper torsion term for ne-ca-ca-ca
        atoms are: N5 C6 C5A C9A
 ** Warning: No sp2 improper torsion term for ca-ca-ca-ha
        atoms are: C5A C7 C6 H6
 ** Warning: No sp2 improper torsion term for ca-ca-ca-ha
        atoms are: C8 C9A C9 H9
 ** Warning: No sp2 improper torsion term for ca-ca-ca-nh
        atoms are: C5A C9 C9A N10
 ** Warning: No sp2 improper torsion term for ca-cd-nh-c3
        atoms are: C9A C10 N10 C1*
 ** Warning: No sp2 improper torsion term for nc-cd-cd-nh
        atoms are: N1 C4A C10 N10

If I proceed while ignoring this, the molecule in question will begin
minimizing in water OK, then exit with an "address error" after several
hundred steps.

If I look through gaff.dat, I can't find improper torsions for the bonds
it's complaining about, so I add the X -X -X -X entry from gaff.dat to my
frcmod file under improper torsions. Strangely, however, it still seems not
to recognize the improper torsions, as it still gives the same warnings in
the leap.log file.

Note: It isn't just that I don't know how to use antechamber or something.
It's worked fine for a number of other small molecules, but seems to be
having problems only with this particular one, for some reason.

Any ideas?

Thanks!
David

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