Custom Search
-- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/> -- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/> On Wed, Mar 4, 2015 at 3:56 AM, FyD <fyd.q4md-forcefieldtools.org> wrote: > Dear Joe, > > A google search at http://archive.ambermd.org/ gives: > http://archive.ambermd.org/201203/0076.html > http://archive.ambermd.org/201208/0388.html > > or just read i.e. > http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff > > perl -p -i.old -e 's/\#\#\!\# //g' script1.ff > grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff > # up to you... > # perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1-new.ff > > & look for ATP1 ATP2 dATP1 dATP2 > > Concerning hydrogen phosphate, dihydrogen phosphate, ...: > See http://q4md-forcefieldtools.org/REDDB/projects/F-90/script4.ff > -> the answer is no > > It looks like data are below ;-) generated using R.E.D. Server Dev./PyRED > This could give you a starting point for other derivatives: > > http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFVTxTnW3LADFIRLutnVSdsCY2OeP4Jz3Z1/P20650.html > > The 3 FF libs for the 3 input molecules: > > http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFVTxTnW3LADFIRLutnVSdsCY2OeP4Jz3Z1/P20650/Data-R.E.D.Server/Mol_MM/Mol_mm1-c1.mol2 > > http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFVTxTnW3LADFIRLutnVSdsCY2OeP4Jz3Z1/P20650/Data-R.E.D.Server/Mol_MM/Mol_mm2-c1.mol2 > > http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFVTxTnW3LADFIRLutnVSdsCY2OeP4Jz3Z1/P20650/Data-R.E.D.Server/Mol_MM/Mol_mm3-c1.mol2 > > There is one missing FF paramter: a big deal ;-) > > http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFVTxTnW3LADFIRLutnVSdsCY2OeP4Jz3Z1/P20650/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown > To be added in a sec using the 'Re_Fit' mode & a frcmod.user input > file (with or without your own mandatory parameters): > http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php > http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf > > Energy decomposition is only carried out - when... there is > (obviously) no missing force filed parameters. > > regards, Francois > > > > Thanks for the links. I took a look at the RED DB info, and it is not > clear > > to me how to manipulate what is in that database to obtain an inorganic > > hydrogen phosphate and inorganic dihydrogen phosphate. Is that possible > > using what is in the F-90 project? > > > > On Tue, Mar 3, 2015 at 4:28 AM, FyD <fyd.q4md-forcefieldtools.org> > wrote: > > > >> Dear Joseph, > >> > >> See also the F-90 REDDB project: > >> http://q4md-forcefieldtools.org/REDDB/projects/F-90/ > >> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff > >> > >> On the top of the FF parameters you can always add your own set of FF > >> paramters. > >> > >> R.E.D. Server/R.E.D. IV are outdated! > >> Please use instead: R.E.D. Server Dev./PyRED at > >> http://q4md-forcefieldtools.org/REDServer-Development/ > >> > >> See http://q4md-forcefieldtools.org/REDServer/images/AnteRED-RED.gif > >> vs > >> http://q4md-forcefieldtools.org/REDServer-Development/images/PyRED.gif > >> > >> PyRED generate a whole force field i.e. not only atomic charges. > >> > >> See the tutorial: > >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php > >> & in particular the last ones: > >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf > >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo5.pdf > >> where you can provide your own atom types (or correct theses > >> automatically generated) and mandatory/missing force field parameters... > >> > >> the mol3 file format is the default file format for FF libraries: > >> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php > >> (it is advantageous for molecular fragments) > >> > >> regards, Francois > >> > >> > >> > >> > I see that the Carlson group has some ADP and ATP parameters that have > >> been > >> > developed for use with ff99SB. However, from my understanding, ff12SB > or > >> > ff14SB are now recommended for protein simulation due to some > >> improvements > >> > in how they treat protein secondary structure. Is anybody aware of > >> whether > >> > the Carlson ADP/ATP parameters have been vetted against ff12SB or > ff14SB, > >> > or if one should expect the modifications that went into those > >> force-fields > >> > to break anything badly if they are used with the Carlson ADP/ATP > >> > parameters? I'm curious because I saw a recent (2013) nice paper from > the > >> > Hummer group on F1-ATPase where they still used the combination of > ff99SB > >> > with these Carlson parameters. > >> > > >> > Also, does anyone know if there are any parameters for HPO42- or > H2PO4- > >> > floating around out there that have been tested with Carlson ADP + > >> > ff99SB/ff12SB/ff14SB? If not then I'll go with the antechamber + RED > >> server > >> > route. > > > > _______________________________________________ > 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/amberReceived on Wed Mar 04 2015 - 22:00:02 PST