CCL: Release of R.E.D. Server 2.0

 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]"
 [venabler__nhlbi.nih.gov]
 I've read through the paper and the two specific CHARMM citations, and have to
 admit my first response over-assumed a reliance on RESP charges.  However, I am
 still concerned about the claim to be to produce complete force field libraries
 for CHARMM, which I initially interpreted as ready-to-use residues in the proper
 topology file format, which wasn't the case.  I believe a claim of being able to
 produce entire CHARMM compatible force field libraries should be demonstrated
 much more completely.
 This quote from the cited paper itself raises question about the level of CHARMM
 and OPLS compatibility:
 "Indeed, RESP and ESP charge values derived using R.E.D. are fully
 compatible with Amber and GLYCAM force fields, (40-47) and can be used in CHARMM
 and OPLS force field based simulations as well. (17-20)"
 References 19 and 20 are not really demonstrations of the exact use of R.E.D.,
 but use CHELPG for the initial charges, which are further adjusted for CHARMM
 compatibility.
 Reading further, it seems the burden of choosing the correct LJ types, and
 thereby the mapping to angle and dihedral terms, is left completely up to the
 end user, which I see as a major weakness.  Thus, the type independence may pose
 a problem, in that novel bonding geometries can be created for which there are
 no angle and dihedral parameters during the user mediated atom typing process.
 With respect,
 --
 Rick Venable     5635 FL/T906
 Membrane Biophysics Section
 NIH/NHLBI Lab. of Computational Biology
 Bethesda, MD  20892-9314   U.S.A.
 (301) 496-1905   venabler AT nhlbi*nih*gov
 On 11/4/10 10:09 PM, "Barry Hardy barry.hardy*o*vtxmail.ch"
 <owner-chemistry|,|ccl.net> wrote:
 Sent to CCL by: FyD [fyd : q4md-forcefieldtools.org]
 Dear Rick Venable,
 R.E.D. means RESP and ESP charge Derivation.
 The R.E.D. Tools and R.E.D. Server do not only deal with _RESP_
 charges but with _ESP_ charges using various algorithms used in MEP
 computation. And ESP charges are used in FFs different from AMBER FFs...
 Then, charge derivation is the first step - charge validation is done
 in a second step.
 See http://www.ncbi.nlm.nih.gov/pubmed/20574571 & references
 cited herein.
 This is why we wrote
 "R.E.D. Server is a web service designed to automatically derive RESP
 and ESP charges, and to build force field libraries for new
 molecules/molecular fragments. R.E.D. Server provides to computational
 biologists involved in AMBER, CHARMM, GLYCAM & OPLS force field based
 biological studies the software and hardware required for charge
 derivation and force field library building."
 regards, Francois
 > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]"
 [venabler!=!nhlbi.nih.gov]
 > Given that RESP/ESP methods are **not** used for the development of
 > CHARMM force fields (a fragment approach similar to OPLS is used),
 > the compatibility of molecules with RESP-based charges with the rest
 >  of the CHARMM force fields is somewhat questionable.  The use of
 > other approaches, notably the CHARMM General force field (CGenFF),
 > is recommended instead of ad hoc web servers for extending the
 > CHARMM force field to new molecules.
 >
 > I did not see anything on the q4md site which discussed this, or
 > that gave any hints about validation of the molecular descriptions
 > produced in the context of CHARMM and its distributed force fields.