VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Tue Jun 12 2007 - 11:35:09 CDT

Francesco,

Francesco Pietra schrieb:
> As I have a computational program that affords ESP
> RESP and CRESP charges reliably for a molecule that
> was cut into fragments and recomposed (with a check of
> dipole moments), is it possible to insert manually
> into paratool the charges so obtained (instead of
> computing them again by the procedure that you
> suggested)? Of course, I have a graphic control of
> which is which about all atoms, hydrogens included
> (and a control of the conformation). I am talking of
> molecules of 50-300 atoms, so that the manual transfer
> would not be too difficult.
>
You can simply put in the charges manually under Edit->"Atom properties".
Alternatively, you can also provide an XBGF file containing the charges
which you could probably generate from your files using a script. Just
load one of your molecules as base molecule and save it as xbgf. Then
you can take a look at the file. You would want to edit the 13th field
in the ATOM records.
For your convenience I attached a simple xbgf example file.
But since the result of your Paratool session will be CHARMM topology
and parameter files you could also edit these if the only thing you want
is charges.
> My computational program does not allow using the
> various FF, such as GAFF, which of my main interest.
> With the partial charges manually transferred as above
> said, I would like to try to go further on with
> VMD/NAMD using GAFF.
>
I'm not quite sure what your goal is. If you transfer the charges into
molecules used in Paratool, you will be able to write out a CHARMM
topology file containing the charges. This doesn't get you any closer to
simulating the using GAFF force field.
Again: VMD doesn't care about parameters and NAMD needs parameter files
as input. If you want to simulate the CHARMM FF you'll need CHARMM files
if you want to simulate AMBER/GAFF you will need AMBER/GAFF parameter
files. Since you want to use GAFF I would highly recommend that you
rather use AMBER's Antechamber tools (available for free). Within
Antechamber you can do all necessary file conversions, run RESP and you
can combine the appropriate files (including charges). I'm not at all
saying that it is easy and I have never done it myself, but there are
people doing it. The results will be proper AMBER/GAFF files that you
can use in simulation engnes like NAMD. Even if you want do do difficult
custom stuff, I suppose it is better and easier to stay within the GAFF
world since this is the FF of your choice. Paratool is (at this time)
mostly intended for CHARMM parameters.
> Incidentally, I got a bit confused by the second page
> of your "Paratool User's Guide", i.e., the way you
> decomposed aspartate. What I see is acetate and
> glycine as components.
>
I do't see any glycine I see N-methylacetamide. If you chop away HR3 of
N-methylacetamide and H2 of acetate and draw a bond between the two
associated carbons you'll have fused backbone and side chain.

Jan

> Thanks
>
> francesco pietra
>
>
>
>
> --- Jan Saam <jan.saam_at_charite.de> wrote:
>
>
>> Dear Francesco,
>>
>> your questions were not improper at all, I have just
>> been *very* busy with
>> other things so that I didn't find time to answer
>> earlier...
>>
>> Regarding question 1:
>> In paratool you can import an ascii file containing
>> the cartesian Hessian
>> using the menu: Hessian->"Import raw cartesian
>> Hessian". You can compute
>> the essian with your favourite QM package and
>> convert it into the
>> following form:
>> For a 10-atom molecule you should have 30 lines each
>> containing 30 values.
>> Since the Hessian is symmetric you may also omit the
>> upper diagonal.
>>
>> Before you load the Hessian you must provide
>> paratool with the according
>> optimized geometry. By default paratool expects a
>> gaussian logfile but you
>> can also load a pdb instead.
>>
>> Note that Paratool is in an early state of
>> development thus somoe
>> important features are still incomplete.
>>
>> Regarding question 2:
>> Except for the paratool plugin VMD does not
>> understand force fields at
>> all. VMD is a viewing and analyzing tool and doesn't
>> need the FF info
>> (yet*). NAMD is a MD simulation engine that
>> understands CHARMM, Gromacs
>> and AMBER parameters. I'm not sure about GAFF but I
>> think the files are in
>> the same format as AMBER so NAMD should be able to
>> handle it.
>>
>> * I agree that there are many desireable application
>> where it would be
>> beneficial if VMD understood force fields. We are
>> working on this...
>>
>> I hope this helps,
>> Jan
>>
>>
>> ---------------------------
>> Jan Saam
>> Institute of Biochemistry
>> Charite Berlin
>> Monbijoustr. 2
>> 10117 Berlin
>>
>>
>> +49 30 450-528-446
>> saam_at_charite.de
>>
>>
>>> Either I am bothering developers and subscribers
>>>
>> with
>>
>>> improper questions, or paratool/gaff are not in
>>>
>> common
>>
>>> use at vmd, so that noone is able to answer.
>>>
>> Though,
>>
>>> more and more problems can't be attacked with
>>> classical MD with parameters for only
>>> nucleotides/proteins/carbohydrates/"lipids".
>>>
>>> Thus, I posed two questions in a three weeks
>>>
>> period
>>
>>> that remained unanswered. Here again:
>>>
>>> 1)Is it possible to provide (manually) the data
>>> paratool needs using a QM code that is neither
>>> Gaussian or Gamess?
>>>
>>> 2)If I understand, the GAFF FF can be imported
>>>
>> into
>>
>>> VMD. Correct?
>>>
>>> That would save me the time of installing NAMD/VMD
>>>
>> to
>>
>>> try myself, perhaps to learn that the answer is NO
>>>
>> to
>>
>>> question (1), a problem that I could not
>>>
>> circumvent
>>
>>> otherwise.
>>>
>>> Thanks
>>>
>>> francesco pietra
>>>
>>>
>>>
>>>
>>>
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-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de