Hello Justin, Thanks for the reply. Sorry to say but I chose the GROMOS force field as for that topology of the ligands could be prepared by PRODRG and I followed tutorials available for Gromacs and most of them used GROMOS forcefield and for starting, parameters used in the tutorials helped me to create .mdp file for my problem. I may be wrong in such choice of forefield. I tried yesterday installing Amber utility for gromacs but when I tried to generate topology of protein with Mangnese, It was giving same error as Mn is not present in its database as also mentioned in the following website http://ffamber.cnsm.csulb.edu/. Any help ? I am really thankful to you for ur time and patience. Regards
onetwo wrote: > Thanks Justin for the help, > > I have Manganese in my protein with other two ligands at the active site. > I am using GROMOS96 43a1 force field. > > Mangnese may have topology similar to Magnesium 2+, What I found is that Assuming a transition metal "may" be similar to another species is probably a pretty poor assumption. Prepare for lots of criticism if you proceed with that thought. > I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I > calculate the nonbond_params for ffG43a1nb.itp. > Refer to the other GROMOS papers for how they derive parameters for small molecules. I've never seen a demonstration of transition metal parameterization under these force fields, though. Perhaps you should be using an AMBER force field that contains Mn2+. Any particular reason you think you need GROMOS? > For both the other two ligands which contains phosphate and enol groups, I > was able to create topology using PRODRG server. Please pay careful attention to the second paragraph here: http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips -Justin > > Regards > > onetwo wrote: > > Hello All, > > > > I am new in this field, and I want to do simulation study on one of the > protein conatining a metal ion and study its ability to form co-oridnation > bond with other ligand, which is not defined in GROMOS force field which I > have tried. If this choice of force field is correct for such type of study ? > > > > I have read Gromacs Manual Chapter 5, also I am following this gromacs > mailing list for quite some time to get a help on how to include a new metal > ion or a new ligand in their simulation and they have been refered to refer > to the http://www.gromacs.org/Documentation/How-tos/Parameterization, > > > > but in this its not mentioned that how to actually do parameterization > > > > neither in manual it has been told on how to generate it ( due > apologies,,I know, I may be wrong ) > > > > The manual will not cover every possible topic. Parameterization is described > in the primary literature for the force field you wish you use. "GROMOS" is > not very specific - there are numerous parameter sets within this class of > force field. > > > and it is more difficult for a person like me who doesnt have much > knowledge in this field, so if someone can please help me guiding how to do > parameterisation, I know this is not a trivial task, but still help in this > regard may help many other fellow users besides me. > > Aside from telling you to read all the literature you can, there's not much > more help anyone can do to help you. You haven't described very well what > your system is. What kind of functional groups are in your ligand? If the > functional groups are shared with existing parameters, then you'll have a > rather easy time constructing a topology. What type of metal ion is it? If > you're dealing with a transition metal, using a standard MM force field may > not work very well. Note the "Exotic Species" heading on the page you quoted > above. > > -Justin > > > Thanks in advance > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- 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 > > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 Go to Previous message | Go to Next message | Back to Messages ASCII (ASCII)Greek (ISO-8859-7)Greek (Windows-1253)Latin-10 (ISO-8859-16)Latin-3 (ISO-8859-3)Latin-6 (ISO-8859-10)Latin-7 (ISO-8859-13)Latin-8 (ISO-8859-14)Latin-9 (ISO-8859-15)W. European (850)W. European (CP858)W. European (HPROMAN8)W. European (MACROMAN8)W. European (Windows-1252)Armenia (ARMSCII-8)Baltic Rim (ISO-8859-4)Baltic Rim (WINDOWS-1257)Cyrillic (866)Cyrillic (ISO-8859-5)Cyrillic (KOI8-R)Cyrillic (KOI8-RU)Cyrillic (KOI8-T)Cyrillic (KOI8-U)Cyrillic (WINDOWS-1251)Latin-2 (852)Latin-2 (ISO-8859-2)Latin-2 (WINDOWS-1250)Turkish (ISO-8859-9)Turkish (WINDOWS-1254)Arabic (ISO-8859-6,ASMO-708)Arabic (WINDOWS-1256)Hebrew (856)Hebrew (862)Hebrew (WINDOWS-1255)Chinese Simplified (GB-2312-80)Chinese Simplified (GB18030)Chinese Simplified (HZ-GB-2312)Chinese Simplified (ISO-2022-CN)Chinese Simplified (WINDOWS-936)Chinese Trad.-Hong Kong (BIG5-HKSCS)Chinese Traditional (BIG5)Chinese Traditional (EUC-TW)Japanese (SHIFT_JIS)Japanese (EUC-JP)Japanese (ISO-2022-JP)Korean (ISO-2022-K R)Korean (EUC-KR)Thai (TIS-620-2533)Thai (WINDOWS-874)Vietnamese (TCVN-5712)Vietnamese (VISCII)Vietnamese (WINDOWS-1258)Unicode (UTF-7)Unicode (UTF-8)Unicode (UTF-16)Unicode (UTF-32) | Full Headers Reply Reply All Forward Forward Mail Search WelcomeInboxNewFoldersMail Options
-- 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
