Dear Karl,
thank you very much for your reply !
I know that this issue is not trivial. The number of answers
from Amber community to my first/second email also nicely illustrates this
fact :))
Meanwhile I found something relevant here:
http://server.ccl.net/cgi-bin/ccl/message.cgi?1997+08+23+001
But as you see it is pretty old but there are some interesting directions
like to:
http://cns-online.org/v1.21/
Thinker
Regarding "my research" here I also discover this beautiful SW repository:
http://www.schrodinger.com/
etc.
To obtain quickly some overview about actual State Of the Art regarding to
my particular problem, I sent to CCL my question which I am attachning
below. If I get some valuable info here I will send it also to Amber forum
since I think that this is really "hot" topic in general ...
Best regards,
Marek
----------MY QUESTION TO CCL
FORUM----------------------------------------------------------------
Dear all,
I would like to simulate carbosilanes and later their complexes with
organic macromolecules using Amber software.
Unfortunately Amber forcefields do not contain proper ff parameters for
silicon.
In spite of this fact there is still possibility to simulate my Si-based
molecules in Amber
but I have to find proper parameters (e.g. bond, angle, dihedral)
somewhere elsewhere ...
I need ff parameters for Si in this contexts:
C-C-C-Si, Si-O-C-C, C-Si-C-H etc.
So I see here two solutions:
A)
To import relevant parameters from another forcefields like CVFF, PCFF,
MM2, MM3 ...
Regarding to this point it would be nice to have some routine which could
be able to convert
one forcefield file XYZ to ff file written in Amber format. If possible
not to
transform just text formating of the source XYZ ff file with respect of
Amber formating,
but also to transform properly the parameters values with respect to
eventual diferences in units or analytic
formulas for interatomic forces.
B)
To derive all the necessary parameters using some intelligent (probably
quantum mechanics based) software which could be able
to do this analysis for small residua provided for example in PDB format.
Again would be nice to have this parameters
in format compatible with Amber ff.
I am kindly asking for any (even only partial) information regarding to
this topic or just for redirecting to
relevant information resources. Of course that I will be grateful not only
for info related to some appropriate SW
which can help me regarding to A) or B) but I will also appreciate any
info based on own experiences, strategies, suggestions, warnings ...
regarding to this topic.
Best regards,
Marek
--------------------------------------------------------------------------------------------------
Dne Mon, 06 Apr 2009 09:39:31 +0200 Karl Kirschner
<kkirsch.scai.fraunhofer.de> napsal/-a:
> Hi Marek,
>
> There is no easy solution for setting up your silicon compound. The best
> solution would be to develop your own parameters, which then would give
> you a
> feeling for where the weaknesses are in the resulting force field. This
> in
> turn will allow you to judge if there are artifacts in the resulting
> simulation that arise from the force field.
>
> Apart from that you can try to find existing parameters in published
> force
> fields and try to transfer them to AMBER. We are doing this to some
> extent,
> but have found that there are several small "pit falls" due to
> differences in
> the force field equations and the various simulation parameters that each
> program gives as default. If you do this, I suggest that you verify that
> the
> parameters are transferred to AMBER correctly by running minimizations
> (check
> each energy term outputted by each program) and simulations (check to
> see if
> you capture the dynamics correctly) on several different traditional
> molecules (hydrocarbons, alcohols, etc). Once you trust your parameter
> conversion, then move onto your more exotic Si compound.
>
> I would be very cautious in using related carbon parameters, and then
> scaling
> them. I am not sure a single or even multiple scaling factors for
> different
> terms would capture the physics properly. This implies a linear
> relationship
> in parameters for elements, and I have not personal seen that in my work.
>
> Just remember that the results of your simulation are directly
> connected to
> the parameters that you use. If you use bad parameters, you will likely
> have
> bad results.
>
> Cheers,
> Karl
>
> On Wednesday 01 April 2009 19:29, Marek Malý wrote:
>> Dear Amber users,
>> some time ago I sent to this forum the
>> below attached email regarding to calculations of Si-based molecules in
>> Amber.
>> Unfortunately I didn't receive any response till now :((
>> Probably it is not so easy to answer/help here as it is clear to me from
>> what
>> I read about similar problems in this forum.
>>
>> So I have to this story just 2 additional questiones ( hopefully not so
>> complicated as the original one :)) )
>>
>> #1 - as it is clear antechamber/parmchk routine has problem to associate
>> Si atoms
>> with the proper bond, angle, dihedral parameters since Amber
>> forcefileds do not
>> contain this parameters for silicon so it is necessary to look
>> for it
>> somewhere
>> elsewhere and modify properly relevant FRCMOD file. I found this
>> parameters in
>> CVFF a PCFF forcefields so I will try to transport/transfer them
>> for
>> the Amber calculation. Is it a good idea ? What I should to care
>> about ?
>> Probably to check the physical units, check if mathematical
>> expressions for
>> the given type of forces is the same i both forcefields, if not
>> make
>> some relevant transformation
>> of the transfered parameters ?
>>
>> Maybe could be a good/elegant idea to use well known
>> parametrisations/parameters (like for example C-N, C-N-C, C-C-N-C)
>> which are present in CVFF, PCFF but also in Amber ff to calculate
>> some scaling constant/s which can be used for
>> easy transformation of C-Si, C-Si-C ... parameters from CVFF, PCFF
>> into Amber ff. Could be this a good idea ?
>>
>>
>> Another possibility is to use PARMCAL routine - I have never used
>> it
>> till now so it would the case to use it to
>> obtain at least the bond length and angle ff parameters for C-Si,
>> Si-O, C-C-Si, C-Si-O ... bonds/angles ?
>>
>> Any experiences with this ffx->ffy transformations ... are highly
>> welcomed ! I think that this issue could be a very interesting
>> also for the other Amber users.
>>
>> #2 - On contrary it seems to me that antechamber/difcon ... has
>> absolutely
>> no problems with "exotic" Si atoms
>> and for example calculated proper(?) Si partial charges. In PREPIN
>> file (please see attached file), there is
>> no error reported so I just would like to ensure: Is it from this
>> point of view everything really OK - are the calculated
>> Si charges usable ? Also PREPIN file contains info about bond
>> lengths, angles, dihedral angles but this are stricly related
>> to the actual values of the input molecular structure not the true
>> equilibrium ones am I right ?
>>
>>
>> Thanks a lot to anybody for any info or own experience with
>> solving
>> of similar problem or just for reference
>> to relevant information resources (is there for example any
>> apprpriate tutorial available ?) !
>>
>> Marek
>>
>>
>>
>> ####-AN---ORIGINAL---EMAIL
>>
>> ------- Předaná zpráva -------
>> Od: "Marek Malý" <maly.sci.ujep.cz>
>> Komu: amber.ambermd.org
>> Kopie:
>> Předmět: [AMBER] Parametrisation of Silicon based molecules for Amber
>> simulations ?
>> Datum: Fri, 20 Mar 2009 00:49:21 +0100
>>
>> Dear Amber users,
>>
>> I would like to simulate molecules which contain also Si (silicon)
>> atoms.
>> Please see attached fig. "mol01.jpg" or "mol.pdb."
>>
>> I tried to parametrise small "testing" molecule using Antechamber and
>> I have obtained relevant PREPIN ("mol.prepin") and FRCMOD ("mol.frcmod")
>> files.
>> The prepin file is OK and also "Si" atoms were asigned with calculated
>> partial charge etc.
>>
>> But there is problem with FRCMOD file which should be probably
>> interpreted
>> in this case only as
>> an empty template for proper forcefield parameters (bond, angle,
>> dihedrals
>> parameters) which
>> need to be included "manually".
>>
>> Nevertheless I tried to make PRMTOP and INPCRD file (just for the
>> curiosity) and I succeeded,
>> but after reading of this two files by "Chimera" and labeling the
>> element
>> types, the "Si" atoms
>> were asigned with the "LP" label (please see "mol02.jpg") although in
>> PRMTOP file are all "Si" atoms
>> named properly and in section "FLAG AMBER_ATOM_TYPE" is clearly written
>> type "Si". But this is probably
>> question for "Chimera" forum :))
>>
>> It is clear to me that I will have to find a proper forcefield
>> parameters
>> so
>> I am kindly asking for any info, links to relevant databases etc.
>>
>> For example I succeed to simulate this molecule in vacuum with MS
>> software
>> using "Dreiding" forcefield.
>> Could be a good idea to adopt desiderative parameters from this
>> forcefield
>> and incorporate them into my FRCMOD
>> file ?
>>
>> How to decide between for example two slightly different
>> parametrisations
>> which I could find in different data sources ( articles, databases ) ?
>> Is there any highly recommended forcefield database available ?
>>
>>
>> I appreciate any help and advices especially from the experienced
>> researchers.
>>
>>
>> Thank you very much in advance !
>>
>> Marek
>
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Received on Wed Apr 08 2009 - 01:12:03 PDT
