Re: AMBER: Antechamber/formatting question

From: Kara Di Giorgio <>
Date: Fri, 25 Feb 2005 16:43:36 -0800

I'm sorry I didn't see this reply sooner. My suddenly decided that
half of the things from this source were Junk and I didn't notice as
some messages were still coming through.

I'd appreciates some clarifications please:

On Feb 21, 2005, at 8:15 AM, YoungJin Cho wrote:

> I have in a similar situation before, and here's what I got from
> others (esp. from Kristina and Jarrod)
> 1. Get a pdb for your own modified residue. In my case, I used all
> phosphate and sugars all together thus I can make a adduct unit for
> antechamber.

I have a pdb of my drug and a guanine/sugar bound together.

> 2. You can use antechamber but try to use amber atom type(look at
> manual) instead of gaff. In my case, it was easy to compare the
> results. However, there are needs to recheck those atom types by your
> eyes.

I was going to use the antechamber atom types for the drug portion and
the standard amber types for the guanine portion.

> 3. Use your RESP charge (which came from in a different source). Since
> antechamber provides bcc charge that is a kind of Mulliken charge. For
> amber purpose, you'd better use RESP charge. In my case, I ran
> gaussian for my adduct. (I put a methyl group instead of including
> sugar and phosphate groups in this case). And applied RESP method,
> then modify those values into antechamber generated charges. Remember
> that sugar and phosphate groups' charges are constant (same as amber
> paper values).

The main problem I have is generating charges. I can't generate
charges on a partial compound (a residue). Can you do this with RESP?
I don't know how to adjust the charges once the extra atoms are deleted
and the residue created. How do you handle this fact?

> 4. You should generate your own adduct lib file and when you load your
> total pdb(it should contain the same name as your lib indicates), you
> always need to load your lib file.

I understand this part from the various tutorials.

Thanks for helping,

Kara Di Giorgio

> In this step you would be OK with your modified guanine unit.
> Hope this can be your help.
> YoungJin
> On Feb 18, 2005, at 12:20 PM, Kara Di Giorgio wrote:
>> 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.
>> Thanks,
>> 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
>>>> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>>>> 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 |
>>> ==================================================================
>>> ---------------------------------------------------------------------
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Received on Sat Feb 26 2005 - 00:53:00 PST
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