AMBER Archive (2008)

Subject: Re: AMBER: FAD RESP charges and parameters

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Tue Dec 30 2008 - 10:03:17 CST

Hi Francois,
   
  I am so glad to see the list below. I think that they are all helpful to the AMBER community. Thank you. I look forward to utilize some more of the RESP charges and FF parameters in the list when they are available in REDDB in the near future.
   
  In the mean time, I would like to have the following HF/6-31G*//HF/6-31G* (parm94 -> parm99) data if you can kindly E-Mail them to me
  1) FAD (oxidized form with -2 charges on the phosphodiester groups)
  2) NADPH (reduced form with a total of -2 charges)
   
  and i will greatly cite REDDB for these parameters.
   
  My best regards,
   
  Jenk
   
  
FyD <fyd_at_q4md-forcefieldtools.org> wrote:
  Jenk,

> I am currently working on developing RESP charges and FF
> parameters for a substrate and inhibitor of an enzyme in complex
> with FAD and NADPH. Developing RESP charges and FF parameters for AD
> and NADPH will take more of my time. Thus, I will appreciate it if
> you generously provide me with FAD and NADPH RESP charges and their
> FF parameters. If NADPH parameters are not available in REDDB, then
> I'll start thinking about using RESP charges and FF parameters for
> NADPH posted on the AMBER website.

Please, simply do a list of what you need. We have:
FXD(H)(P"-1" or P"-2")
NXD(H)(P"-1" or P"-2")
even more (see the whole list below: cyclic-XMP; Coenz-A; Acetyl-CoA etc..)

All FF libraries based on QM computation + 2 stage RESP fit using:
1) HF/6-31G*//HF/6-31G* (parm94 -> parm99)
or
2) b3lyp/cc-pVTZ SCRF(IEFPCM...)//HF/6-31G** (ff03; Duan et al.)

Each set was generated in a single R.E.D.-IV run in a multi-molecules,
multi-conformations and multi-orientations RESP fit (in RESP
nmol=164). Thus, charge values are perfectly reproducible using
Gaussian, PC-GAMESS/Firefly or GAMESS-US.

> Oh by the whay! How should I cite your RESP charges and FF parameters ?

We will provide the data in R.E.DD.B. (just need the time to make the
data available) Just cite R.E.DD.B. - Nucl. Acids Res. (Database
issue), 2008, D360-D367 + the corresponding R.E.DD.B. code, as all the
data are available in a single complex force field topology database
generated in a single R.E.D.-IV run.

regards, Francois

Whole list:
2008-10-19 23:10 ACOA.mol2
2008-10-19 23:10 ACOAP1.mol2
2008-10-19 23:10 ACOAP2.mol2
2008-10-19 23:10 ADP1.mol2
2008-10-19 23:10 ADP2.mol2
2008-10-19 23:10 AMP1.mol2
2008-10-19 23:10 AMP2.mol2
2008-10-19 23:10 AQP1.mol2
2008-10-19 23:10 AQP2.mol2
2008-10-19 23:10 ATP1.mol2
2008-10-19 23:10 ATP2.mol2
2008-10-19 23:11 CAMPP1.mol2
2008-10-19 23:11 CAMPP2.mol2
2008-10-19 23:11 CCMPP1.mol2
2008-10-19 23:11 CCMPP2.mol2
2008-10-19 23:10 CDP1.mol2
2008-10-19 23:10 CDP2.mol2
2008-10-19 23:11 CGMPP1.mol2
2008-10-19 23:11 CGMPP2.mol2
2008-10-19 23:10 CMP1.mol2
2008-10-19 23:10 CMP2.mol2
2008-10-19 23:10 COA.mol2
2008-10-19 23:10 COAP1.mol2
2008-10-19 23:10 COAP2.mol2
2008-10-19 23:10 COASAC.mol2
2008-10-19 23:11 COASACP1.mol2
2008-10-19 23:11 COASACP2.mol2
2008-10-19 23:10 COASH.mol2
2008-10-19 23:11 COASHP1.mol2
2008-10-19 23:11 COASHP2.mol2
2008-10-19 23:10 COCSAC.mol2
2008-10-19 23:11 COCSACP1.mol2
2008-10-19 23:11 COCSACP2.mol2
2008-10-19 23:10 COCSH.mol2
2008-10-19 23:11 COCSHP1.mol2
2008-10-19 23:11 COCSHP2.mol2
2008-10-19 23:10 COGSAC.mol2
2008-10-19 23:11 COGSACP1.mol2
2008-10-19 23:11 COGSACP2.mol2
2008-10-19 23:10 COGSH.mol2
2008-10-19 23:11 COGSHP1.mol2
2008-10-19 23:11 COGSHP2.mol2
2008-10-19 23:10 COUSAC.mol2
2008-10-19 23:11 COUSACP1.mol2
2008-10-19 23:11 COUSACP2.mol2
2008-10-19 23:10 COUSH.mol2
2008-10-19 23:11 COUSHP1.mol2
2008-10-19 23:11 COUSHP2.mol2
2008-10-19 23:10 CQP1.mol2
2008-10-19 23:10 CQP2.mol2
2008-10-19 23:10 CTP1.mol2
2008-10-19 23:10 CTP2.mol2
2008-10-19 23:11 CUMPP1.mol2
2008-10-19 23:11 CUMPP2.mol2
2008-10-19 23:10 FAD.mol2
2008-10-19 23:10 FADH.mol2
2008-10-19 23:10 FADHP1.mol2
2008-10-19 23:10 FADHP2.mol2
2008-10-19 23:10 FADP1.mol2
2008-10-19 23:10 FADP2.mol2
2008-10-19 23:10 FCD.mol2
2008-10-19 23:10 FCDH.mol2
2008-10-19 23:10 FGD.mol2
2008-10-19 23:10 FGDH.mol2
2008-10-19 23:10 FMN1.mol2
2008-10-19 23:10 FMN1H.mol2
2008-10-19 23:10 FMN2.mol2
2008-10-19 23:10 FMN2H.mol2
2008-10-19 23:10 FUD.mol2
2008-10-19 23:10 FUDH.mol2
2008-10-19 23:10 GDP1.mol2
2008-10-19 23:10 GDP2.mol2
2008-10-19 23:10 GMP1.mol2
2008-10-19 23:10 GMP2.mol2
2008-10-19 23:10 GQP1.mol2
2008-10-19 23:10 GQP2.mol2
2008-10-19 23:10 GTP1.mol2
2008-10-19 23:10 GTP2.mol2
2008-10-19 23:10 NAD.mol2
2008-10-19 23:10 NADH.mol2
2008-10-19 23:10 NADP1.mol2
2008-10-19 23:10 NADP1H.mol2
2008-10-19 23:10 NADP2.mol2
2008-10-19 23:10 NADP2H.mol2
2008-10-19 23:10 NCD.mol2
2008-10-19 23:10 NCDH.mol2
2008-10-19 23:10 NCDP1.mol2
2008-10-19 23:10 NCDP1H.mol2
2008-10-19 23:10 NCDP2.mol2
2008-10-19 23:10 NCDP2H.mol2
2008-10-19 23:10 NGD.mol2
2008-10-19 23:10 NGDH.mol2
2008-10-19 23:10 NGDP1.mol2
2008-10-19 23:10 NGDP1H.mol2
2008-10-19 23:10 NGDP2.mol2
2008-10-19 23:10 NGDP2H.mol2
2008-10-19 23:10 NUD.mol2
2008-10-19 23:10 NUDH.mol2
2008-10-19 23:10 NUDP1.mol2
2008-10-19 23:10 NUDP1H.mol2
2008-10-19 23:10 NUDP2.mol2
2008-10-19 23:10 NUDP2H.mol2
2008-10-19 23:10 RBFLV.mol2
2008-10-19 23:10 RBFLVH.mol2
2008-10-19 23:10 UDP1.mol2
2008-10-19 23:10 UDP2.mol2
2008-10-19 23:10 UMP1.mol2
2008-10-19 23:10 UMP2.mol2
2008-10-19 23:10 UQP1.mol2
2008-10-19 23:10 UQP2.mol2
2008-10-19 23:10 UTP1.mol2
2008-10-19 23:10 UTP2.mol2
2008-10-19 23:10 dADP1.mol2
2008-10-19 23:10 dADP2.mol2
2008-10-19 23:10 dAMP1.mol2
2008-10-19 23:10 dAMP2.mol2
2008-10-19 23:10 dAQP1.mol2
2008-10-19 23:10 dAQP2.mol2
2008-10-19 23:10 dATP1.mol2
2008-10-19 23:10 dATP2.mol2
2008-10-19 23:10 dCDP1.mol2
2008-10-19 23:10 dCDP2.mol2
2008-10-19 23:10 dCMP1.mol2
2008-10-19 23:10 dCMP2.mol2
2008-10-19 23:10 dCOASAC.mol2
2008-10-19 23:11 dCOASACP1.mol2
2008-10-19 23:11 dCOASACP2.mol2
2008-10-19 23:10 dCOASH.mol2
2008-10-19 23:11 dCOASHP1.mol2
2008-10-19 23:11 dCOASHP2.mol2
2008-10-19 23:10 dCOCSAC.mol2
2008-10-19 23:11 dCOCSACP1.mol2
2008-10-19 23:11 dCOCSACP2.mol2
2008-10-19 23:10 dCOCSH.mol2
2008-10-19 23:11 dCOCSHP1.mol2
2008-10-19 23:11 dCOCSHP2.mol2
2008-10-19 23:10 dCOGSAC.mol2
2008-10-19 23:11 dCOGSACP1.mol2
2008-10-19 23:11 dCOGSACP2.mol2
2008-10-19 23:10 dCOGSH.mol2
2008-10-19 23:11 dCOGSHP1.mol2
2008-10-19 23:11 dCOGSHP2.mol2
2008-10-19 23:10 dCOTSAC.mol2
2008-10-19 23:11 dCOTSACP1.mol2
2008-10-19 23:11 dCOTSACP2.mol2
2008-10-19 23:10 dCOTSH.mol2
2008-10-19 23:11 dCOTSHP1.mol2
2008-10-19 23:11 dCOTSHP2.mol2
2008-10-19 23:10 dCQP1.mol2
2008-10-19 23:10 dCQP2.mol2
2008-10-19 23:10 dCTP1.mol2
2008-10-19 23:10 dCTP2.mol2
2008-10-19 23:10 dFAD.mol2
2008-10-19 23:10 dFADH.mol2
2008-10-19 23:10 dFCD.mol2
2008-10-19 23:10 dFCDH.mol2
2008-10-19 23:10 dFGD.mol2
2008-10-19 23:10 dFGDH.mol2
2008-10-19 23:10 dFUD.mol2
2008-10-19 23:10 dFUDH.mol2
2008-10-19 23:10 dGDP1.mol2
2008-10-19 23:10 dGDP2.mol2
2008-10-19 23:10 dGMP1.mol2
2008-10-19 23:10 dGMP2.mol2
2008-10-19 23:10 dGQP1.mol2
2008-10-19 23:10 dGQP2.mol2
2008-10-19 23:10 dGTP1.mol2
2008-10-19 23:10 dGTP2.mol2
2008-10-19 23:10 dNAD.mol2
2008-10-19 23:10 dNADH.mol2
2008-10-19 23:10 dNCD.mol2
2008-10-19 23:10 dNCDH.mol2
2008-10-19 23:10 dNGD.mol2
2008-10-19 23:10 dNGDH.mol2
2008-10-19 23:10 dNTD.mol2
2008-10-19 23:10 dNTDH.mol2
2008-10-19 23:10 dTDP1.mol2
2008-10-19 23:10 dTDP2.mol2
2008-10-19 23:10 dTMP1.mol2
2008-10-19 23:10 dTMP2.mol2
2008-10-19 23:10 dTQP1.mol2
2008-10-19 23:10 dTQP2.mol2
2008-10-19 23:10 dTTP1.mol2
2008-10-19 23:10 dTTP2.mol2

more generally, an infinity of FF libraries can be built...

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