VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Tue Jun 12 2007 - 11:36:46 CDT

Here's the promised XBGF that I forgot to attach previously.
Jan

Francesco Pietra schrieb:
> Jan:
> My second reply to your message.
>
> 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.
>
> 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.
>
> 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.
>
> 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

BIOGRF 332
REMARK NATOM 8
FORCEFIELD DREIDING
FORMAT ATOM (a6,1x,i6,1x,a5,1x,a4,1x,a1,1x,i5,3f10.5,1x,a5,i3,i2,1x,f8.5,1x,f6.3,1x,f6.3,1x,i3,1x,a4)
ATOM 1 O2 ACEH X 1 0.17800 0.00000 -1.34800 OB 0 0 -0.61000 0.200 1.000 8 QMT
ATOM 2 C1 ACEH X 1 0.19100 0.00000 -0.08500 CD 0 0 0.75000 0.200 1.000 6 QMT
ATOM 3 O1 ACEH X 1 1.18400 0.00000 0.69300 OH1 0 0 -0.55000 0.200 1.000 8 QMT
ATOM 4 C2 ACEH X 1 -1.22000 0.00000 0.59000 CT3 0 0 -0.30000 0.200 1.000 6 QMT
ATOM 5 H21 ACEH X 1 -1.78700 -0.88300 0.26300 HA 0 0 0.09000 0.200 1.000 1 QMT
ATOM 6 H22 ACEH X 1 -1.78700 0.88300 0.26300 HA 0 0 0.09000 0.200 1.000 1 QMT
ATOM 7 H23 ACEH X 1 -1.14700 0.00000 1.68400 HA 0 0 0.09000 0.200 1.000 1 QMT
ATOM 8 HO1 ACEH X 1 2.02300 -0.00000 0.15000 H 0 0 0.44000 0.200 1.000 1 QMT
FORMAT CONECT (a6,14i6)
FORMAT ORDER (a6,i6,13f6.3)
CONECT 1 2
ORDER 1 1.000
CONECT 2 1 4 3
ORDER 2 1.000 1.000 1.000
CONECT 3 2 8
ORDER 3 1.000 1.000
CONECT 4 2 5 6 7
ORDER 4 1.000 1.000 1.000 1.000
CONECT 5 4
ORDER 5 1.000
CONECT 6 4
ORDER 6 1.000
CONECT 7 4
ORDER 7 1.000
CONECT 8 3
ORDER 8 1.000
VDW 1 -0.1200 1.7000 -0.1200 1.4000
VDW 2 -0.0700 2.0000
VDW 3 -0.1521 1.7700
VDW 4 -0.0800 2.0600 -0.0100 1.9000
VDW 5 -0.0220 1.3200
VDW 6 -0.0220 1.3200
VDW 7 -0.0220 1.3200
VDW 8 -0.0460 0.2245
LEWIS 1
LEWIS 2
LEWIS 3
LEWIS 4
LEWIS 5
LEWIS 6
LEWIS 7
LEWIS 8
END