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
>>
>>
>>
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>>
>
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--
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 - 02:00:05 PST
