Hi all,
I am trying to write an frcmod file for acetonitrile to use parameters
from the literature. I could only find little information on frcmod
files, neither in the manual nor online so I have a few questions.
I attached an frcmod file I generated with parmchk2 below in order to
facilitate the discussion.
Here go my questions:
* In the MASS card, I have four columns. What are the third and fourth
columns? Is the third one the charge?
* In the NONBON card, are those the same Lennard Jones Parameters A
and B as in the topology files?
* If I specify e.g. NONBON parameters, do I have to do this for all
atom types in my molecule or only for those I actually want to
change? e.g. my molecule has 5 different atom types, but I only want
to change parameters for 2 of them
* Assuming I have to different ligands in my system, that include the
same atom type. Can I assign different parameters to the same atom
type for each ligand? Or do I need to define a new atom type? e.g.
Ligand1 has an atom of charge 0.5 and ligand2 has an atom of the
same type but with a charge of 0.6
I would really appreciate your help!
Best,
Andy
Remark line goes here
MASS
CT 12.010 0.878 same as c3
HC 1.008 0.135 same as hc
...
BOND
CT-HC 330.60 1.097 same as c3-hc, penalty score= 0.0
C -CT 313.00 1.524 same as c-c3, penalty score= 0.0
...
ANGLE
CT-C -O 67.400 123.200 same as c3-c -o , penalty score= 0.0
CT-C -N 66.790 115.180 same as c3-c -n , penalty score= 0.0
...
DIHE
CT-C -N -H 4 10.000 180.000 2.000 same as X -c
-n -X , penalty score= 0.0
CT-C -N -CT 1 0.000 0.000 -2.000 same as c3-c
-n -c3
CT-C -N -CT 1 1.500 180.000 1.000 same as c3-c
-n -c3, penalty score= 0.0
...
IMPROPER
CT-N -C -O 1.1 180.0 2.0 Using the
default value
C -CT-N -H 1.1 180.0 2.0 Using the
default value
C -H -N -H 1.1 180.0 2.0 Same as X -X
-n -hn, penalty score= 6.0 (use general term))
...
NONBON
CT 1.9080 0.1094 same as c3
On 04/05/2017 06:08 PM, Andreas Tosstorff wrote:
> Dear all,
>
>
> thank you for your replies! As David pointed out, setting up the
> simulation was not the problem, but it's the separation of the two
> solvents, as seen in the attached pictures.
>
> After the suggested google search I came across a paper titled "New
> Six-site Acetonitrile Model for Simulations of Liquid Acetonitrile and
> its Aqueous Mixtures" by NIKITIN and LYUBARTSEV from 2007 (attached to
> this mail).
>
> They report that they were able to succesfully simulate
> water-acetonitrile mixtures with their acetonitrile model. They
> furthermore state that their model can easily be included into AMBER.
>
> So how do I do this?
>
> Do I write an .frcmod and .lib file for acetonitrile using the
> parameters (Lennard-Jones parameters, charge, what else?) they
> published and then rebuild my system in tleap?
>
>
> This is completely new to me so I would really appreciate your help!
>
>
> Best,
>
> Andy
>
>
> On 04/05/2017 05:00 PM, David Cerutti wrote:
>> You will not have an extra time with this if you want your simulation
>> to go
>> a long time. For starters you can use the AddToBox utility in amber/bin
>> (run with no arguments to see the list of things you can do). That will
>> help you randomly mix acetonitrile and water initially (make sure to
>> minimize before starting dynamics).
>>
>> But if you simulate just a few hundred acetonitriles and a thousand
>> waters
>> (or whatever the ratio needs to be), then check after 50ns or so, and
>> find
>> that they separate (which appears likely) you have as DAC said an
>> imbalance
>> in your FF and a parameter development problem.
>>
>> Once you get your solvents to stay mixed, round II: protein in solvent
>> mixture. You could very well find that the protein gets coated in
>> acetonitrile and that the acetonitrile gets leached out of solution
>> in the
>> process. To determine whether THAT is realistic or not you will need
>> the
>> right kind of experimental data.
>>
>> Dave
>>
>> On Apr 5, 2017 10:48 AM, "Sowmya Indrakumar" <soemya.kemi.dtu.dk> wrote:
>>
>>> Hi Andreas,
>>> I am not sure if this is feasible.
>>> Since you already know the ratio, you can do the following
>>> 1.solvate you protein
>>> 2.replace some of the water with the other molecule. For instance,
>>> *addions* randomly replaces water with the ion you give.
>>> Regards
>>> Sowmya
>>> ________________________________________
>>> From: David A Case [david.case.rutgers.edu]
>>> Sent: Wednesday, April 05, 2017 4:37 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] Acetonitrile Water Mix
>>>
>>> On Wed, Apr 05, 2017, Andreas Tosstorff wrote:
>>>> I am trying to simulate a protein in a 60% acetonitrile, 40% water
>>> mixture.
>>>> I observed that the two solvents arrange in layers rather than to
>>>> form a
>>>> homogeneous mix. See the attached pictures and input files.
>>>> Any advice on how to perform simulations with solvent mixtures?
>>> Sounds like you already know how to perform the simulations. If
>>> these two
>>> liquids are supposed to be miscible, then there is likely an
>>> inbalance in
>>> your
>>> force field. Try a Google search on something like "acetonitrile water
>>> force
>>> field" to see what others have done in simulating this sort of mixture.
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
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>
>
>
> _______________________________________________
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Thu Apr 06 2017 - 01:30:02 PDT
