Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I tried to do the same, I got some errors during tpr file constructing. So I really don't know how to do it.
best regards > > > jorge_quint...@ciencias.uis.edu.co wrote: >> Dear Justin >> >> I removed the semicolons but my calculations don't work. The problem is >> how can I add the other parameters -like bonds, angles and dihedrals- >> for >> B-state. I've tried to add it, but I get some problems to obtain the >> tpr >> file. Thanks again. >> > > Please read the manual, section 5.7.4. I don't see why you need to mutate > bonded interactions for a solvation free energy calculation. For toluene, > there > is even a tutorial available at the following link. It is for a different > force > field, but should still be useful: > > http://md.chem.rug.nl/education/Free-Energy_Course/index.html > > Also, from your original topology, you should not turn off charges and L-J > interactions simultaneously; doing so will lead to very large errors. > These > transformations should be done separately. Please refer to the wiki page > on the > Gromacs site and the numerous discussions in the list archive about proper > procedure. The tutorial above will also help. > > -Justin > >> [ bonds ] >> 1 2 1 --> how can I write the B-state parameters?? >> ............. >> [ angles ] >> 2 1 3 1 ??? >> ............. >> [ dihedrals ] >> 2 1 4 5 3 ????? >> >> >> Best regards >> >>> >>> jorge_quint...@ciencias.uis.edu.co wrote: >>>> Dear all. >>>> >>>> I've tried to calculate solvatin free energy using amber force field >>>> and >>>> gromacs but unfourtunately I can't include the parameters for B type. >>>> Can >>>> somebody help me with that, I send you a top file. >>>> >>> All of your B-state parameters are commented out. Remove the >>> semicolons. >>> >>> -Justin >>> >>>> Best regards, >>>> >>>> >>>> Jorge R. Quintero >>>> Grupo de Investigación en Fisicoquímica Teórica y Experimental >>>> (GIFTEX) >>>> Universidad Industrial de Santander >>>> Escuela de Química >>>> Bucaramanga, Santander - Colombia >>>> >>> -- >>> ======================================== >>> >>> 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 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 > 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 > -- 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
