Re: [AMBER] will AM1-BCC good enough for GAFF lipids?

From: Vlad Cojocaru <>
Date: Fri, 02 Dec 2011 11:03:15 +0100

And here are the references I mentioned ...

J Chem Phys.
2008 Mar 28;128(12):125103.
Biomolecular simulations of membranes: physical properties from
different force fields.
Siu SW
Vácha R
Jungwirth P
Böckmann RA

J Comput Chem.
<> 2007
Performance of the general amber force field in modeling aqueous POPC
membrane bilayers.
Jójárt B
Martinek TA

J Comput Chem. <> 2008 Jan
Structure and dynamics of phospholipid bilayers using recently developed
general all-atom force fields.
Rosso L
Gould IR

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:
>>> 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
>>> 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
>>> 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
>>> 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 mailing list

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]
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Received on Fri Dec 02 2011 - 02:30:02 PST
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