Re: [gmx-users] parameterization of new metal ion
On Thu, May 17, 2012 at 11:47 AM, priya thiyagarajan priya.thiyagaraja...@gmail.com wrote: Respected sir, i want to add metal ions Ni2+ and co2+ during my simulation. can anyone help me how to set parameters to define new ion Ni2+ and co2+ in gromacs forcefield.. i edited in ions.itp file and tried but i got error atomtype not found.. You need to modify the .rtp file as well. Follow this: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Anirban can anyone please explain me elaborately how to set parameters .. please help me with your answer.. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] parameterization of new metal ion
hello sir, thanks for your kind reply.. while setting new parameters for metal ion NI2+ i edited my ions.itp by including the following lines.. [ moleculetype ] ; molname nrexcl NI 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 NI2+1 NI NI 1 257.9339 also edited .rtp file by including the following lines [ NI ] [ atoms ] NI NI2+ 2.0 0 [ bonds ] [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type but still i am getting the error Fatal error: Atomtype NI2+ not found can you tell me how to solve this error.. thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] parameterization of new metal ion
On 5/17/12 5:12 AM, priya thiyagarajan wrote: hello sir, thanks for your kind reply.. while setting new parameters for metal ion NI2+ i edited my ions.itp by including the following lines.. [ moleculetype ] ; molname nrexcl NI 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 NI2+1 NI NI 1 257.9339 also edited .rtp file by including the following lines [ NI ] [ atoms ] NI NI2+ 2.0 0 [ bonds ] [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type but still i am getting the error Fatal error: Atomtype NI2+ not found can you tell me how to solve this error.. Parameters for all atom types must be listed in ffnonbonded.itp, and atomtypes.atp if you're having pdb2gmx build the topology (which is also where the .rtp entry comes into play). -Justin -- Justin A. Lemkul, Ph.D. 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Parameterization of a molecule containing a radical (oxygen)
Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find its PubChem entry here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs As you can see, the problem of this molecule is its O radical; this, and the N belonging to the cycle too. My lab would really benefit from the parameterization (for the AMBER force field) of tempol, since we commonly use it in our NMR experiments. We don't know how to treat the oxygen radical and the N bound to it, though. If this parameterization is impossible to do we will give up, but we would like to be sure about it. Thanks in advance for any answer you could provide. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs -- Simone Cirri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Parameterization of a molecule containing a radical (oxygen)
Simone Cirri wrote: Hi all, I have a question regarding a new parameterization: actually, I'm wondering whether or not it is possible to do it. The molecule is tempol; you cand find its PubChem entry here http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs As you can see, the problem of this molecule is its O radical; this, and the N belonging to the cycle too. My lab would really benefit from the parameterization (for the AMBER force field) of tempol, since we commonly use it in our NMR experiments. We don't know how to treat the oxygen radical and the N bound to it, though. If this parameterization is impossible to do we will give up, but we would like to be sure about it. Thanks in advance for any answer you could provide. http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994loc=ec_rcs This would not be a trivial molecule to parameterize. You could start by using antechamber (available free as part of AmberTools), since it allows you to tune multiplicity (-m flag). Otherwise, the existing force fields may not provide a suitable atom type for the O radical or its effects on the rest of the molecule. I still don't know if parameterization would be possible for a standard MM force field (though it very well might), but this might get you started. -Justin -- Simone Cirri -- 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Parameterization
You could use GLYCAM which is in AMBER so the parameters are already there in the correct format (but not in the AMBER ported to GROMACS) and convert that to GROMACS topology. It'll save you some time :) I had problems converting the improper dihedral that holds the NAc group planar using amb2gmx.pl so keep an eye on it. Good Luck, Oliver On 15 November 2010 22:15, Anthony Cruz Balberdi anthony.cr...@upr.eduwrote: Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use ambertools to find the necessary force field parameters and generate an AMBER topology. After that use acpype to transform the amber topology to a GROMACS topology. From the GROMACS topology the create an itp file to use in your GROMACS TOPOLOGY. To better understand what I said please read the reference for the force field, the GROMACS manual and the RED tutorial. Best Regards, Anthony On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA yuvrajthe...@gmail.com wrote: How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Parameterization
How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Parameterization
Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use ambertools to find the necessary force field parameters and generate an AMBER topology. After that use acpype to transform the amber topology to a GROMACS topology. From the GROMACS topology the create an itp file to use in your GROMACS TOPOLOGY. To better understand what I said please read the reference for the force field, the GROMACS manual and the RED tutorial. Best Regards, Anthony On Mon, Nov 15, 2010 at 5:13 PM, YUVRAJ UBOVEJA yuvrajthe...@gmail.com wrote: How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] parameterization of ligand
Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field. Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Regards Subarna Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-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
Re: [gmx-users] parameterization of ligand
subarna thakur wrote: Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field. Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Chapter 5 of the manual is dedicated to topology format and organization. -Justin Regards Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ gmx-users mailing listgmx-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 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 listgmx-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
