Hi Tom!! Thanks for the information. I went through the paper and added the new O3 atom type. One unusual thing I noticed was that the sum of the partial charges on the atoms of AT P at the last column of http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile is -12.7145. How come fractional? and the hydrogens of phosphate are missing. How can it be overcome?
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot <t.pig...@bristol.ac.uk> wrote: > From the Carlson et al. paper where these ATP parameters were published >> and >> > through choosing the appropriate amber_X atom types from the .atp (and the > corresponding values for these types in the nb and bon .itp files). As I > mentioned previously you need to add a new O3 atom type to these files based > on the information in the Carlson paper. > > If you have a look at one of the entries from the ffamberXX.rtp file and > work out how this is used by pdb2gmx it should become clear what you need to > do to add the ATP to the forcefield. > > Cheers > > Tom > > > --On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury < > iitd...@gmail.com> wrote: > > >> Hi Thomas ! >> >> Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon >> values etc. values. Where to get these values >> >> >> Chandan >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> >> On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot <t.pig...@bristol.ac.uk> >> wrote: >> >> Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult >> the GROMACS manual (Chapter 4) for the equations to convert the >> parameters into GROMACS format. >> >> I would also say that the easiest way would be to create a new entry in >> the .rtp and then also add the appropriate bonded parameters into the >> bon.itp file, making sure to include the bonded parameters for the new O3 >> atom type. Do note that you need to also add this new atom type for the >> O3 oxygen into the .atp file and the non-bonded parameters for the atom >> type into the nb.itp file. >> >> You can also add entries into the .hdb to allow pdb2gmx to add the >> appropriate hydrogens to your ATP if so desired. If not, your input pdb >> for pdb2gmx will need to have these hydrogens already included. >> >> Cheers >> >> Tom >> >> Chandan Choudhury wrote: >> >> >> Hello gmx users, >> I need to use ATP's parameter for amber port in gromacs. The atp.prep and >> frcmod.phos for ATP can be found at >> http://www.pharmacy.manchester.ac.uk/bryce/a<http://www.pharmacy.manchester.ac.uk/bryce/amber> > > *mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr >> -e spc_25_eq.edr -g spc_25_eq.log -append yes* > > mber <http://www.pharmacy.manchester.ac.uk/bryce/amber>. How can I use it >> in >> ffamber. >> The program amb2gmx.pl <http://amb2gmx.pl> needs amber to be installed, >> which is not present. Same with ACPYPI. >> >> >> Any suggestion will be very helpful. >> >> Chandan >> >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> >> -- >> Thomas Piggot >> University of Bristol, UK. >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > > > ---------------------- > TJ Piggot > > t.pig...@bristol.ac.uk > University of Bristol, UK. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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