Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, As for the GROMOS FF, I've included a link to the paper describing the most recent (AFAIK) version of the FF in one of the recent mailing list massages. Good luck, Ran On Sat, 18 Apr 2009 15:56:11 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Josmar R. da Rocha wrote: Dear Ran, Thanks for answering and sorry to take so long to reply. After your response I went seach for more information about that. What I read here in the list is that some people uses antechamber to generate am1-bcc charges (or RESP charges using Gaussian program) and convert the output files to a .top file (using the amb2gmx.pl script) that can be used in gromacs, however, nobody says the kind of ff they intend to use that charges with. Do these type of charges can also be used with Gromos96 ff ( 43a1)? Thanks in advance! The amb2gmx was created to handle AMBER-to-GROMACS conversion. It is unlikely that it would be useful for ffG43a1. Since 43a1 is a united-atom force field, you have to compensate for the fact that nonpolar hydrogen atoms are absent. Furthermore, quantum charge calculation is not a necessary component of Gromos96 parameter derivation. See, for example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. /r.fried...@bioc.uzh.ch/* escreveu: De: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Para: bije...@yahoo.com.br, Discussion list for GROMACS users gmx-users@gromacs.org Data: Sexta-feira, 27 de Março de 2009, 17:35 Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take
Re: [gmx-users] Combining LJ and buckingham potential
Hello Osmair, Perhaps you can try using the [ nonbond_params ] [ pairs ] sections of the TOP file? How did you define these interactions in your TOP file? --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Apr 17, 2009 at 22:51, osmair oliveira osmai...@hotmail.com wrote: Hi, I have tried to simulate a crystal in water solvent, however I found the error: ERROR 0 [file new-topol3.top, line 19]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) So, my question: How can I use or define LJ potential (for water) and buckingham potential (for a crystal) in the same *.top, *.itp? Thanks, Osmair V. Oliveira Ph.D. Student Brazil ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Combining LJ and buckingham potential
Hi Omer, My nonbond_params are: [ nonbond_params ] ; For crystal (buckingham potential) O O 2 2196413.486.7112690.96 Ce O 2 191696.3982.8491968.294 CeCe 2 0 00 ; For water (LJ potential) HOW 1 0 0 OW O 1 0.0024331696 1.83399e-06 Thanks Osmair Date: Sun, 19 Apr 2009 14:47:24 +0300 Subject: Re: [gmx-users] Combining LJ and buckingham potential From: omer...@gmail.com To: gmx-users@gromacs.org Hello Osmair, Perhaps you can try using the [ nonbond_params ] [ pairs ] sections of the TOP file? How did you define these interactions in your TOP file? --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Apr 17, 2009 at 22:51, osmair oliveira osmai...@hotmail.com wrote: Hi, I have tried to simulate a crystal in water solvent, however I found the error: ERROR 0 [file new-topol3.top, line 19]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) So, my question: How can I use or define LJ potential (for water) and buckingham potential (for a crystal) in the same *.top, *.itp? Thanks, Osmair V. Oliveira Ph.D. Student Brazil _ Faça já uma busa e ganhe um wink do Messenger. Está esperando o que? É grátis! http://www.ibud.com.br/___ gmx-users mailing listgmx-users@gromacs.org http://www.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] (no subject)
Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] (no subject)
He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] (no subject)
Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 listgmx-users@gromacs.org http://www.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] (no subject)
He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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://www.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] (no subject)
It always show the common error Invalid order for directive defaults.I suppose it is because I have defined an atom belonging to two groups . What do you mean by freezing subgroups of atoms within a molecule ? I just wonder how to make it ?Can you give me some examples? Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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://www.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 listgmx-users@gromacs.org http://www.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] (no subject)
He, Yang wrote: It always show the common error Invalid order for directive defaults.I suppose it is because I have defined an atom belonging to two groups . What do you mean by freezing subgroups of atoms within a molecule ? I just wonder how to make it ?Can you give me some examples? The error is unrelated to your freezegrps. See here: http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Your index groups should be fine. A subgroup refers to select atoms within a molecule, as in backbone of the protein, headgroups of lipids, or some such similar idea. As I said before, your use of freezegrps and index groups should, in theory, be fine. -Justin Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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://www.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
RE: [gmx-users] (no subject)
Hi Justin, In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand and it works but if I want to freeze some atoms in this single strand, it seems that I have no choice but choose the position restraints. The freezegrps seems not to work for that. But the error for the position restraints always is fragmentation fault and can not be fixed although many methods have been tried. I don't know whether this is a bug in the gromacs cause I have followed the steps in manual to simulate a case(about speptide) in manual with position restraints while it still doesn't work. I am confused about that. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 4:41 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: It always show the common error Invalid order for directive defaults.I suppose it is because I have defined an atom belonging to two groups . What do you mean by freezing subgroups of atoms within a molecule ? I just wonder how to make it ?Can you give me some examples? The error is unrelated to your freezegrps. See here: http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Your index groups should be fine. A subgroup refers to select atoms within a molecule, as in backbone of the protein, headgroups of lipids, or some such similar idea. As I said before, your use of freezegrps and index groups should, in theory, be fine. -Justin Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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.
Re: [gmx-users] (no subject)
He, Yang wrote: Hi Justin, In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand and it works but if I want to freeze some atoms in this single strand, it seems that I have no choice but choose the position restraints. The freezegrps seems not to work for that. But the error for the position restraints always is fragmentation fault and can not be fixed although many methods have been tried. So then the following is true: freezegrps = DNA works fine freezegrps = (your groups) gives Invalid order for directive defaults That would make no sense. The error comes from the topology, not anything specified in the .mdp file, so I don't understand. I don't know whether this is a bug in the gromacs cause I have followed the steps in manual to simulate a case(about speptide) in manual with position restraints while it still doesn't work. I am confused about that. I doubt it is a bug; this would be pretty prohibitory for most users. It may be specific to your system. If you can provide details of your system, compilers, which Gromacs version you are using (provided in a new thread that has a noticeable subject line), you may be able to sort that issue out. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 4:41 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: It always show the common error Invalid order for directive defaults.I suppose it is because I have defined an atom belonging to two groups . What do you mean by freezing subgroups of atoms within a molecule ? I just wonder how to make it ?Can you give me some examples? The error is unrelated to your freezegrps. See here: http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Your index groups should be fine. A subgroup refers to select atoms within a molecule, as in backbone of the protein, headgroups of lipids, or some such similar idea. As I said before, your use of freezegrps and index groups should, in theory, be fine. -Justin Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine. -Justin I hope what I said is clear to you all and I really appreciate your any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
RE: [gmx-users] (no subject)
Hi Justin, My version is a little old just 3.3.1 and I work in the LINUX system . As for my system, I have four single CG DNA model put in the box randomly to see whether they can hybridize with the matched single strand while I need to keep the two strand fixed through fixing one or two atoms in that single strand . Hence, I use the position restraints to fix the two atoms in one single strand . Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 5:28 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand and it works but if I want to freeze some atoms in this single strand, it seems that I have no choice but choose the position restraints. The freezegrps seems not to work for that. But the error for the position restraints always is fragmentation fault and can not be fixed although many methods have been tried. So then the following is true: freezegrps = DNA works fine freezegrps = (your groups) gives Invalid order for directive defaults That would make no sense. The error comes from the topology, not anything specified in the .mdp file, so I don't understand. I don't know whether this is a bug in the gromacs cause I have followed the steps in manual to simulate a case(about speptide) in manual with position restraints while it still doesn't work. I am confused about that. I doubt it is a bug; this would be pretty prohibitory for most users. It may be specific to your system. If you can provide details of your system, compilers, which Gromacs version you are using (provided in a new thread that has a noticeable subject line), you may be able to sort that issue out. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 4:41 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: It always show the common error Invalid order for directive defaults.I suppose it is because I have defined an atom belonging to two groups . What do you mean by freezing subgroups of atoms within a molecule ? I just wonder how to make it ?Can you give me some examples? The error is unrelated to your freezegrps. See here: http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Your index groups should be fine. A subgroup refers to select atoms within a molecule, as in backbone of the protein, headgroups of lipids, or some such similar idea. As I said before, your use of freezegrps and index groups should, in theory, be fine. -Justin Thank you very much. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 3:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi Justin, In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group. Alright, so what's the error? You should be able to freeze subgroups of atoms within a molecule; I've done it several times in different instances. -Justin Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Sunday, April 19, 2009 1:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) He, Yang wrote: Hi all users, I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this: [God] 21 22 [Bad] 61 62 And I have defined the atom numbering 21, 22, 61,62 in gro file like this : 2MOM bT 21 0.805 1.330 3.914 2MOM bT 22 0.448 1.572 3.576 4ICE bT 61 0.805 4.330 3.914 4ICE bT 62 0.448 4.572 3.576 I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs . Are you assuming an error, or have you tried it and actually received an error? Use these groups as the freezegrps in the .mdp file and try it. It should be fine.
Re: [gmx-users] (no subject)
He, Yang wrote: It always show the common error Invalid order for directive defaults There can only be one [defaults] section in your whole .top file. Usually, an attempt to mix two force fields results in provoking this error. You should inspect your .top file carefully, searching for this directive it it and the files you are #including. If you can't find it, you may need to post that .top file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] HF/6-31G** ESP derived charges to replace PRODRGassigned ones
How can you calculate computationally charges for molecules containing phosphates? -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the reproduction of experimentally-observed behavior if I do not have experimental data for my system? 3-I also would like to know from users dealing with protein-ligand interactions studies what do you consider a good approach to address this problem? Based on what I read I'd have a tendency to use HF/6-31G** ESP derived charges (with necessary changes as to make it united-atom charges and scaling that to a integer number for each group). Please, let me know if that strategy would be as good as a disaster! Thank you very much for the attention. Josmar Rocha Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the
