And here are the references I mentioned ...
J Chem Phys.
<
http://www.ncbi.nlm.nih.gov/pubmed?term=Rainer%20Boeckamnn%20and%20GAFF#>
2008 Mar 28;128(12):125103.
Biomolecular simulations of membranes: physical properties from
different force fields.
Siu SW
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22Siu%20SW%22%5BAuthor%5D>,
Vácha R
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22V%C3%A1cha%20R%22%5BAuthor%5D>,
Jungwirth P
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22Jungwirth%20P%22%5BAuthor%5D>,
Böckmann RA
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22B%C3%B6ckmann%20RA%22%5BAuthor%5D>.
J Comput Chem.
<
http://www.ncbi.nlm.nih.gov/pubmed?term=Martinek%20and%20GAFF#> 2007
Sep;28(12):2051-8.
Performance of the general amber force field in modeling aqueous POPC
membrane bilayers.
Jójárt B
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22J%C3%B3j%C3%A1rt%20B%22%5BAuthor%5D>,
Martinek TA
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22Martinek%20TA%22%5BAuthor%5D>.
J Comput Chem. <
http://www.ncbi.nlm.nih.gov/pubmed/17910006#> 2008 Jan
15;29(1):24-37.
Structure and dynamics of phospholipid bilayers using recently developed
general all-atom force fields.
Rosso L
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22Rosso%20L%22%5BAuthor%5D>,
Gould IR
<
http://www.ncbi.nlm.nih.gov/pubmed?term=%22Gould%20IR%22%5BAuthor%5D>.
On 12/02/2011 10:58 AM, Vlad Cojocaru wrote:
> There are a couple of references for deriving GAFF parameters for lipids ...
> Rainer Boeckman and coworkers and Tamas Martinek and co-workers did some
> nice work with different lipids .. Please check those papers before
> starting to derive your own parameters .... They derived RESP charges
> for the lipids. I don't know why would you use AM1-BCC charges instead
> of RESP charges. Especially, since for lipids GAFF parameters are far
> from being ideal (see references mentioned) you probably don't want to
> introduce another level of approximation by substituting RESP with
> AM1-BCC charges.
>
> Anyhow, there is no need to derive new parameters if they already exist ...
>
> A recent application of the Jojart& Martinek parameters for POPC is
> published in PLoS Comput. Biol. (Cojocaru et al. August 2011)
>
> Good luck
> Vlad
>
> On 12/02/2011 10:03 AM, Albert wrote:
>> Hi Francois:
>> Thanks again for such detailed explanations. I do learned a lot these
>> days. I will try it recently.
>>
>> Best wishes& nice weekend
>>
>> Albert
>>
>> On 12/02/2011 09:02 AM, FyD wrote:
>>> Dear Albert,
>>>
>>>> I've got another question about the partial charge calculation in
>>>> AMBER. I found that it use RESP for HF/6-31G* for Amber FF. I am
>>>> wondering, is CHARMM 27 or CHARMM36 use the same methods for partial
>>>> charge calculation? I may also use CHARMM FF in amber in the near future.
>>> CHARMM FF do not use RESP charges; See for instance, the following
>>> tutorial: http://mackerell.umaryland.edu/~kenno/tutorial/
>>> It seems that RESP charges are only for AMBER FF although a RESP model
>>> for OPLS does exist: it even uses the RESP program from the AMBER
>>> distribution. See
>>> http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19990415)20:5%3C483::AID-JCC2%3E3.0.CO;2-4/abstract
>>>
>>> Then, once this is said, you find many articles in the literature
>>> where CHARMM users and even developers DO use molecular electrostatic
>>> potential (MEP)-based charges.
>>>
>>> R.E.D. III.x and R.E.D. Server/R.E.D. IV do not only derive RESP
>>> charges; but are able to derive ESP charges based on different
>>> algorithms (CHELPG, Connolly surface; if you use GAMESS you could
>>> modify the source code and use the GEODESIC algo. by Spackman) for the
>>> grid of points in MEP computation.
>>> See
>>> http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19960115)17:1%3C1::AID-JCC1%3E3.0.CO;2-V/abstract
>>>
>>> Whatever the charge model you will select - you will have to
>>> demonstrate that it is suitable for your problem. If you do use a
>>> CHARMM FF, I would start by using the CHELPG algo and ESP charges;
>>> i.e. the ESP-C1 charge model in R.E.D.; if you use R.E.D. Server
>>> Development you will be able to use the ESP-Y1 charge model.
>>> See http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
>>> We plan to release more "user defined options" in R.E.D. Server
>>> development - letting users to choose between various basis sets in
>>> the geometry optimization and MEP computation steps... You can also
>>> easily modify the source code of R.E.D. III.x and include the basis
>>> set and theory level of you choice; if you do not know how to do it;
>>> just ask in the Amber or q4md-fft mailing list and we will do it for
>>> you.
>>>
>>> regards, Francois
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Dec 02 2011 - 02:30:02 PST
