[gmx-users] Re: gmx-users Digest, Vol 83, Issue 188
k al fuc0, c1, m, ... > >1 4 3 2 2 0.0 167.40.0 167.4 ; imp NBS > > CBQ H8M HBS > >4 1 5 6 2 0.0 167.40.0 167.4 ; imp CBQ > > NBS OBT CAV > >6 4 9 7 2 0.0 167.40.0 167.4 ; imp CAV > > CBQ CBE CAN > > > > -- > > > 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 > > > > > -- > > Message: 2 > Date: Sat, 26 Mar 2011 11:29:56 -0600 > From: Warren Gallin > Subject: [gmx-users] mdrun cannot append to file larger than 2Gb > To: Discussion list for GROMACS users > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got > an error that I have never seen before, to whit: > > Program mdrun_mpi, VERSION 4.5.3 > Source code file: > /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: > 1727 > > Fatal error: > The original run wrote a file called 'traj.xtc' which is larger than 2 GB, > but mdrun did not support large file offsets. Can not append. Run mdrun with > -noappend > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > > I've never had a problem with extending runs like this before. > > As suggested, I then ran with -noappend set, and it ran fine, creating a > new set of numbered files for the ouput. I am assuming that I'll be able to > combine the trajectory files at the end of the process. > > Have I missed some fine point in compiling that has left mdrun a little > broken? > > Thanks, > > Warren Gallin > > -- > > Message: 3 > Date: Sat, 26 Mar 2011 14:08:55 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] mdrun cannot append to file larger than 2Gb > To: Discussion list for GROMACS users > Message-ID: <4d8e2bb7.2020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Warren Gallin wrote: > > Hi, > > > > Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and > got an error that I have never seen before, to whit: > > > > Program mdrun_mpi, VERSION 4.5.3 > > Source code file: > /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: > 1727 > > > > Fatal error: > > The original run wrote a file called 'traj.xtc' which is larger than 2 > GB, but mdrun did not support large file offsets. Can not append. Run mdrun > with -noappend > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > > I've never had a problem with extending runs like this before. > > > > As suggested, I then ran with -noappend set, and it ran fine, creating a > new set of numbered files for the ouput. I am assuming that I'll be able to > combine the trajectory files at the end of the process. > > > > Correct. > > > Have I missed some fine point in compiling that has left mdrun a little > broken? > > > > Possibly, but it probably depends more on your system's architecture than > anything you did. There is a configure option --disable-largefile (which > should > be the default), so you'd have to check config.log to see if this was > changed to > --enable-largefile based on what the configuration script found. Or you > can > re-compile and see if configuration fails with --enable-largefile and > understand > the reason. > > -Justin > > > Thanks, > > > > Warren Gallin-- > > 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 > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry >
[gmx-users] amide partial charges
Hi May I ask if anyone know a good reference for partial charges of "-CH2-NH-CO-CH2-CH2"(amide)? I plan to use gromos 53A6 force field. I searched the internet quite a while but not sure what is the best. I will be appreciated if you could recommend one with the reference paper. Thank you in advance! Cheers! Xueming -- 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] Re: make_ndx
such as residue 288 which is has C when I tried a C, it's inclusive residue 288. while tried the ri 288 & a C, it showed me Group is empty. Thanks, On Sun, Mar 27, 2011 at 1:42 PM, ZHAO Lina wrote: > Hi, > > Does the "!" in make_ndx work? > > "|" and "&" work, but seems "!" not work. > > I met something weird, > suppose > I choose a C11, which is from ri 1-111. > if use > a C11, the atom is 111 > if use > a C11 & ri 1-111, the atom is 111 > if use > a C11 & ri 101-111, the atom is 5. Which is expected to be 10, so this > situation is wrong. > if use > a C11 & ri 1-100, the atom is 100, which is right. > > I want to know how can I use "!" to exclude some group? > > This mistake is reproducible and I didn't figure it out (Even I examined > the .gro). > > Thanks for any suggestion. > > lina > -- 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] make_ndx
Hi, Does the "!" in make_ndx work? "|" and "&" work, but seems "!" not work. I met something weird, suppose I choose a C11, which is from ri 1-111. if use a C11, the atom is 111 if use a C11 & ri 1-111, the atom is 111 if use a C11 & ri 101-111, the atom is 5. Which is expected to be 10, so this situation is wrong. if use a C11 & ri 1-100, the atom is 100, which is right. I want to know how can I use "!" to exclude some group? This mistake is reproducible and I didn't figure it out (Even I examined the .gro). Thanks for any suggestion. lina -- 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] heat capacity in 4.5.3 and 4.0.7
Dear all, I am trying to calculate Cv of a pure alkane 125 molecules with actual density, and here is what I have done: 1- Cv: Run NVT > g_energy>select T and Etot=total energy As I issue g_energy *.edr Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000369503) And when I choose –nmol XXX Heat Capacity Cv: 13.4007 J/mol K (factor = 0.0462137) - Do I have to use –nmol? What would be the unit with –nmol ? and as I issue g_energy using 4.5.3 Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 0 Heat capacity at constant volume Cv:341.734 J/mol K and with -nconstr # of bonds Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 19 Heat capacity at constant volume Cv:262.746 J/mol K - From this I am guessing what 4.0.7 reports is not correct!? but still what I am getting from 4.5.3 is far from actual reported value (around 170). I guess I am missing something..! or Is the difference acceptable? g_energy says: you will need to give the number of constraints per molecule –nconstr - so I need to count how many bonds are fixed in the molecule as I am setting constraints= all-bonds? The way to this is counting no. of bonds? What about macromolecules? Is there an easier way of finding number of constraints? 2- Cp: I did NPT, g_energy *.edr -nmol XXX -nconstr (4.5.3) I want to select T and enthalpy but since enthalpy is not on the list I select total-energy (which is Etot I think) and pv terms but g_energy is still giving Cv! PropertyEnergy terms needed --- Heat capacity Cp (NPT sims):Enthalpy, Temp Energy Average Err.Est. RMSD Tot-Drift --- Total Energy86.1571 0.0851.55565 -0.0944531 (kJ/mol) Temperature 300.074 0.075.77219 0.318146 (kJ/mol) pV 15.8128 0.0611080.82 -0.249203 (kJ/mol) Temperature dependent fluctuation properties at T = 300.074. #constr/mol = 19 Heat capacity at constant volume Cv:325.067 J/mol K Can you please guide me where the problem lies? --- again Cv : to compare with constraints=none but still -nconstr should be on otherwise I values are more off. Total Energy132.418 0.0511.77314 0.144794 (kJ/mol) Temperature 300.008 0.0524.502090.15866 (kJ/mol) Temperature dependent fluctuation properties at T = 300.008. #constr/mol = 20 Heat capacity at constant volume Cv:442.016 J/mol K 3- Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp Isothermal compressibility: Vol, Temp Adiabatic bulk modulus: Vol, Temp Since volume appears for calculation of the above properties , does this imply only NPT results in these properties? and wanted to make sure what 4.5.3 reports is reliable.. Many thanks for you time! Best, -- 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] How can I convert Gromacs ouput to Desmond input file??
On 27/03/11, 김현식 wrote: > > > > > > > > > Dear experts, > > Hi, I used to gromacs for MD, but there is need to make desmond file from > gromacs output. > > > > > > > > When linked against an installation of VMD, GROMACS can read and write any file format that VMD can do. For all I know, that might include Desmond's formats. It will certainly include something that Desmond can handle - even if that's a PDB pseudo-trajectory, for which you don't need VMD. Mark > > > > > > > > > > > > -- 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] How can I convert Gromacs ouput to Desmond input file??
Dear experts, Hi, I used to gromacs for MD, but there is need to make desmond file from gromacs output. If there is anyone who know how to this, please let me know. Thank you very much. -Hyun--- 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] RMSD Calculation
Nancy wrote: Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html If there's some reason you can't get that to work, then don't simply re-post the same original question. Iterative calls to g_rms are quite straightforward to script. -Justin Thank you very much, Nancy -- 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
[gmx-users] RMSD Calculation
Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy -- 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] Re: Alcohol Dehydrogenase MD simulation....Reg
Kishore wrote: Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .itp file. I have been using the topologies generated by PRODRG server for NADPH as i could not make it comply with the inbuilt residue template library topologies. In this topologies generated by PRODRG there is a directive called [ dihedrals ] and it listed out all the dihedrals with comment lines showing proper and improper dihedrals, but this seems to differ from the way the the topologies are defined in the gromacs inbuilt template library which only lists out the impropers. Does this make any difference in terms of grompp interpreting them during the preprocessing? I am herein pasting a section of that dihedrals and a snapshot of the NADPH molecule with the atom names labelled so that you can see that the impropers you mentioned in your reply are infact mentioned in the .itp file I am using. The three improper dihedrals you have mentioned are highlighted below...please correct me in case if i am getting the meaning wrong..Sorry for flooding with long posts, but I am in a great need for some help on this. [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 4 3 2 2 0.0 167.40.0 167.4 ; imp NBS CBQ H8M HBS 4 1 5 6 2 0.0 167.40.0 167.4 ; imp CBQ NBS OBT CAV 6 4 9 7 2 0.0 167.40.0 167.4 ; imp CAV CBQ CBE CAN That looks like the correct function form on reasonable atoms - but you'd have to check the naming scheme yourself. Do the charges look reasonable to your chemical experience? How does a simulation of just NADPH in vacuo go? In a small water box? Mark -- 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] Best Program for Simulating Lipid Bilayers in Water
Hi All, I heard that LAMMPS is supposedly good for simulating lipid bilayers in water. I haven't used LAMMPS before; does anyone know if it would be worth to try it in addition to Gromacs? Thanks in advance, Nancy -- 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] mdrun cannot append to file larger than 2Gb
Warren Gallin wrote: Hi, Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit: Program mdrun_mpi, VERSION 4.5.3 Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727 Fatal error: The original run wrote a file called 'traj.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I've never had a problem with extending runs like this before. As suggested, I then ran with -noappend set, and it ran fine, creating a new set of numbered files for the ouput. I am assuming that I'll be able to combine the trajectory files at the end of the process. Correct. Have I missed some fine point in compiling that has left mdrun a little broken? Possibly, but it probably depends more on your system's architecture than anything you did. There is a configure option --disable-largefile (which should be the default), so you'd have to check config.log to see if this was changed to --enable-largefile based on what the configuration script found. Or you can re-compile and see if configuration fails with --enable-largefile and understand the reason. -Justin Thanks, Warren Gallin-- 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 -- 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
[gmx-users] mdrun cannot append to file larger than 2Gb
Hi, Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit: Program mdrun_mpi, VERSION 4.5.3 Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727 Fatal error: The original run wrote a file called 'traj.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I've never had a problem with extending runs like this before. As suggested, I then ran with -noappend set, and it ran fine, creating a new set of numbered files for the ouput. I am assuming that I'll be able to combine the trajectory files at the end of the process. Have I missed some fine point in compiling that has left mdrun a little broken? Thanks, Warren Gallin-- 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] Re: Alcohol Dehydrogenase MD simulation....Reg
Please choose a relevant subject line and do not reply to the entire digest; it confuses the archive. Kishore wrote: Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .itp file. I have been using the topologies generated by PRODRG server for NADPH as i could not make it comply with the inbuilt residue template library topologies. In this topologies generated by PRODRG there is a directive called [ dihedrals ] and it listed out all the dihedrals with comment lines showing proper and improper dihedrals, but this seems to differ from the way the the topologies are defined in the gromacs inbuilt template library which only lists out the impropers. Does this make any difference in terms of grompp interpreting them during the preprocessing? I am herein pasting a section of that dihedrals and a snapshot of the NADPH molecule with the atom names labelled so that you can see that the impropers you mentioned in your reply are infact mentioned in the .itp file I am using. Gromacs separates proper and improper dihedrals in [dihedrals] directives, presumably for convenience. Having one or two directives with proper contents does not make a difference. If, however, PRODRG is assigning parameters that the force field library does not, that just sounds like typical PRODRG behavior - its parameters are often incorrect and one has to know the proper way to handle re-assigning parameters. Bonded parameters are often more correct than charges and charge groups from PRODRG, which are wrong in all the cases I've ever seen. http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin The three improper dihedrals you have mentioned are highlighted below...please correct me in case if i am getting the meaning wrong..Sorry for flooding with long posts, but I am in a great need for some help on this. [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 4 3 2 2 0.0 167.40.0 167.4 ; imp NBS CBQ H8M HBS 4 1 5 6 2 0.0 167.40.0 167.4 ; imp CBQ NBS OBT CAV 6 4 9 7 2 0.0 167.40.0 167.4 ; imp CAV CBQ CBE CAN -- 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
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 160
Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .itp file. I have been using the topologies generated by PRODRG server for NADPH as i could not make it comply with the inbuilt residue template library topologies. In this topologies generated by PRODRG there is a directive called [ dihedrals ] and it listed out all the dihedrals with comment lines showing proper and improper dihedrals, but this seems to differ from the way the the topologies are defined in the gromacs inbuilt template library which only lists out the impropers. Does this make any difference in terms of grompp interpreting them during the preprocessing? I am herein pasting a section of that dihedrals and a snapshot of the NADPH molecule with the atom names labelled so that you can see that the impropers you mentioned in your reply are infact mentioned in the .itp file I am using. The three improper dihedrals you have mentioned are highlighted below...please correct me in case if i am getting the meaning wrong..Sorry for flooding with long posts, but I am in a great need for some help on this. [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 4 3 2 2 0.0 167.40.0 167.4 ; imp NBS CBQ H8M HBS 4 1 5 6 2 0.0 167.40.0 167.4 ; imp CBQ NBS OBT CAV 6 4 9 7 2 0.0 167.40.0 167.4 ; imp CAV CBQ CBE CAN On Wed, Mar 23, 2011 at 8:37 AM, wrote: > Send gmx-users mailing list submissions to >gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit >http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to >gmx-users-requ...@gromacs.org > > You can reach the person managing the list at >gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Alcohol Dehydrogenase MD simulationReg (Mark Abraham) > 2. Re: Parameterization of a molecule containing a radical > (oxygen) (Justin A. Lemkul) > 3. unit of surface tension, KJ/mol? (Elisabeth) > 4. Re: unit of surface tension, KJ/mol? (Justin A. Lemkul) > 5. Re: unit of surface tension, KJ/mol? (Elisabeth) > 6. Re: unit of surface tension, KJ/mol? (Justin A. Lemkul) > 7. Re: unit of surface tension, KJ/mol? (Elisabeth) > > > -- > > Message: 1 > Date: Wed, 23 Mar 2011 11:46:30 +1100 > From: Mark Abraham > Subject: Re: [gmx-users] Alcohol Dehydrogenase MD simulationReg > To: Discussion list for GROMACS users > Message-ID: <4d8942e6.8020...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 23/03/2011 4:38 AM, Kishore wrote: > > Dear All, > > > > I had been in the look out for someone who has a reasonable amount of > > expertise in dealing with the MD simulation of an Alcohol > > Dehydrogenase. I have a problem dealing with the NADPH. I was unable > > to maintain the planarity of the carboxamide of the nicotinamide > > moiety in the simulation as a result of which important sidechain > > hydrogen bonds are being lost in the simulation. Is such behaviour > > expected or is it because of the non quantum mechanical treatment of > > the NADPH molecule that these kind of situations occur? If anyone has > > some experience please share it. > > Classical MD simulations use improper dihedrals to maintain such > planarity. You can see this in the amide links in a peptide backbone, > for example. Each set of four co-planar atoms (three arranged around a > central one) needs an improper dihedral. So you need H-N-C-H, N-C-O-Cr4 > and C-Cr4-Cr5-Cr3 (where the ring carbons are named Cr and numbered > clockwise from N) in order for the carboxamide to stay coplanar with the > aromatic ring > > > -- > > Message: 2 > Date: Tue, 22 Mar 2011 20:56:41 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Parameterization of a molecule containing a >radical (oxygen) > To: Discussion list for GROMACS users > Message-ID: <4d894549.80...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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=137994&loc=ec_rcs > > < > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=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 commo
