AMBER Archive (2005)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Tue Oct 18 2005 - 14:21:39 CDT

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 | 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&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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