Thanks Tom. Some how only the negative charges were being added in spreadsheet. So, I got charge around -12. I am simulating 1QHH. It has ATP in it, the structure of the ligand in the rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP with hydrogen.
-- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot <t.pig...@bristol.ac.uk>wrote: > Are you sure you added it up correctly? I get a number very close to -4. > > There is no hydrogen on the gamma phosphate as it was parameterised in this > way. If the environment in which your ATP is located suggests that the gamma > phosphate should be protonated then you need to use other ATP parameters > which include this hydrogen (such as those in the GROMOS forcefield). > > > Cheers > > Tom > > Chandan Choudhury wrote: > >> 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<mailto: >> 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 <mailto: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 <mailto:t.pig...@bristol.ac.uk>> >> wrote: >> >> Not sure about amb2gmx.pl <http://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> <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 >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> ---------------------- >> TJ Piggot >> >> t.pig...@bristol.ac.uk <mailto:t.pig...@bristol.ac.uk> >> >> University of Bristol, UK. >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > 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 >
-- 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
