Re: AMBER: Antechamber/formatting question

From: Kara Di Giorgio <>
Date: Fri, 18 Feb 2005 10:20:40 -0800

I've gotten my residue through antechamber and can import it into
xleap. I can't, however, figure out how to make it into a residue.
I've tried to use prepgen and a mainchain file, but I guess I don't
understand how to format the mainchain file. Whenever I use any type
of mainchain file to create the prepin file, I can no longer generate a
frcmod file. When I try to import the prepin file into xLeap, i get a
fatal error and it bombs. Does anyone have any suggestions? Any help
would be greatly appreciated.


Kara Di Giorgio
University of the Pacific

On Feb 5, 2005, at 11:17 AM, David A. Case wrote:

> On Fri, Feb 04, 2005, Kara Di Giorgio wrote:
>> I'm trying to model a minor groove binding agent bound to a 10-mer DNA
>> strand. I created the DNA in nucgen and am planning on creating a
>> custom unit consisting of the guanine/compound bound together and then
>> modifying the DNA-pdb to insert the custom unit instead of the
>> guanine.
>> As the DNA strand is symmetrical, one compound will be on each
>> strand.
>> (This seemed to be the method suggested in the tutorial "Simulating a
>> Solvated Protein that Contains Non-Standard Residues".)
>> 1. Is this a reasonable approach to take? Is there another way to do
>> this that is easier?
> yes.
>> 2. I'm trying to create the custom unit using antechamber. I have a
>> previous (very old) pdb file that has the guanine/compound already
>> covalently attached. I've tried to delete all other information from
>> the pdb and then run it through antechamber. It fails when trying to
>> assign bond types. I get the message:
>> Running: /usr/local/amber/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
>> Cannot successfully assign bond type for this molecule, please :
>> (1) double check the structure (the connectivity) and/or
>> (2) adjust atom valence penalty parameters in APS.DAT, and/or
>> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> Leave out the "-j full" flag to bondtype; equivalently, add the "-j 5"
> flag to
> the antechamber command.
> You have two residues in your input pdb file. This is OK, but note
> that the
> output files created will merge everything into a single residue:
> antechamber
> really only works on single residues.
>> and then it goes on and tries to run divcon where it fails due to no
>> convergence.
> You have a "dangling" phosphate group at the end of your molecule.
> Divcon
> (and antechamber) need a "full" molecule, with all valencies filled.
> You
> may also need to tell antehcamber the overall charge of your molecule,
> if it
> is not neutral.
> Note that you are trying a very big system (90 atoms). Even with
> correct
> input, it may be tricky to get SCF convergence. If so, you may have
> to split
> the molecule into two parts, and run each separately.
> I would suggest leaving off the sugar-phosphate part of the molecule
> (replacing C1' with a hydrogen, or a methyl group), and use the
> standard
> Amber parameters for that. And you sure have an unusual chemistry
> here!
> Be sure to check that antechamber is giving reasonable results,
> especially
> around N14.
> ...good luck...dac
>> p.s. I'm running on a MacG4 PowerBook through an X11 terminal window
> It doesn't look like these are Mac-specific problems: I got the same
> behavior
> you did on my Windows machine.
> --
> ==================================================================
> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA |
> ==================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Feb 18 2005 - 18:53:01 PST
Custom Search