AMBER Archive (2005)

Subject: Re: AMBER: Antechamber/formatting question

From: YoungJin Cho (young.j.cho_at_vanderbilt.edu)
Date: Mon Feb 21 2005 - 10:15:32 CST

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.
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.
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).
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.

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: case_at_scripps.edu
>> 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 | http://www.scripps.edu/case
>> ==================================================================
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