Re: [gmx-users] Top file modification
On 3/21/13 6:30 AM, Shima Arasteh wrote: Dears, As I read in some other messages in mailing list, it is supposed to modify bonds, angles and dihedrals in top file to define a peptide bond for the last and first residues as well as other peptide bonds. I am wondering if it is necessary to define pairs too? If pairs are a necessary part of the force field, then yes. Look at the formulation of peptide bonds that you have not messed with to learn what is expected. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Top file modification
Dears, As I read in some other messages in mailing list, it is supposed to modify bonds, angles and dihedrals in top file to define a peptide bond for the last and first residues as well as other peptide bonds. I am wondering if it is necessary to define pairs too? Thanks in advance. Sincerely, Shima From: Justin Lemkul To: Shima Arasteh Cc: Discussion list for GROMACS users Sent: Tuesday, March 19, 2013 9:11 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh wrote: Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? > > >And I don't know that if I don't add all bonds or dihedrals what would happen? >How would I be sure that I have added all modifications completely? > > All you're doing is creating a peptide bond like any other. Its description should be identical to any other peptide bond in the protein. An incorrect or incomplete description of the newly created peptide bond would mean an unreliable physical model that would either crash or produce spurious results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Top file modification
On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh wrote: > Would you please let me know if it is acceptable to add dihedrals and > angles and bonds? and not to add any pairs to the top? just deleting the > pairs which are added by pdb2gmx incorrectly to the terminus? > > > And I don't know that if I don't add all bonds or dihedrals what would > happen? How would I be sure that I have added all modifications completely? > > All you're doing is creating a peptide bond like any other. Its description should be identical to any other peptide bond in the protein. An incorrect or incomplete description of the newly created peptide bond would mean an unreliable physical model that would either crash or produce spurious results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Top file modification
Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? Sincerely, Shima From: Justin Lemkul To: Shima Arasteh Sent: Tuesday, March 19, 2013 9:00 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:28 PM, Shima Arasteh wrote: :) > > >In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and >topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top >file. Is there any better ideas? > > Manual modification in that case is probably reasonably safe, as long as you are careful to use parameters that are appropriate for all bonded and nonbonded interactions that change as a result of the modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Top file modification
:) In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas? Thanks for your reply. Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Tuesday, March 19, 2013 8:51 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh wrote: > > Dear users, > >I modified my top file, because I didn't want some bonds. So I deleted them >and changed charges on some atoms. >I want to go on with such a top file, however I am not sure that these changes >are implemented properly or not. Would you please let me know if what I did is >right or not? > >And how would I be sure about the proper modifications? > > Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure. What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. "Somebody on the Internet told me it was OK" is generally not an acceptable defense ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Top file modification
On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh wrote: > > > Dear users, > > I modified my top file, because I didn't want some bonds. So I deleted > them and changed charges on some atoms. > I want to go on with such a top file, however I am not sure that these > changes are implemented properly or not. Would you please let me know if > what I did is right or not? > > And how would I be sure about the proper modifications? > > Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure. What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. "Somebody on the Internet told me it was OK" is generally not an acceptable defense ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Top file modification
Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Thanks in advance for all your beneficial suggestions. Sincerely, Shima -- 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
