Re: [gmx-users] gmxcheck
Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this) Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul wrote: > > > On 11/4/13 7:37 AM, Ankita Naithani wrote: > >> I do have the .mdp file. Main thing I was concerned about were details >> like >> number of water molecules added and number of counter ions added. Does >> gmxdump output that information? >> >> > Yes, buried in a long list of other things. Trivial details like that are > simply read from the last few lines of the .top though, so there's no need > to invoke any other accessory programs. > > -Justin > > > >> >> >> On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul wrote: >> >> >>> >>> On 11/4/13 7:14 AM, Ankita Naithani wrote: >>> >>> Hi Justin, >>>> >>>> Thank you for your reply. I did give the .tpr file but the job >>>> terminated >>>> after few frames only. Also, if that is not helpful, do you have any >>>> >>>> >>> There are no frames in a .tpr file. I suspect you're simply issuing the >>> command incorrectly, but since you haven't shown us what you're doing, >>> there's little else to suggest. >>> >>> >>> suggestions to recover the essential information which you would >>> include >>> >>>> as >>>> part of methods? >>>> >>>> >>>> The .mdp file has all the instructions for the simulation. If you >>> don't >>> have that around for whatever reason (very bad to get rid of such >>> files!), >>> all of the same information is recorded in the beginning of the .log file >>> or can be written out by gmxdump. In the latter case, make sure to >>> redirect the output to a file rather than just have thousands of lines of >>> text blur by in the terminal. >>> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Ankita Naithani -- 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] gmxcheck
I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul wrote: > > > On 11/4/13 7:14 AM, Ankita Naithani wrote: > >> Hi Justin, >> >> Thank you for your reply. I did give the .tpr file but the job terminated >> after few frames only. Also, if that is not helpful, do you have any >> > > There are no frames in a .tpr file. I suspect you're simply issuing the > command incorrectly, but since you haven't shown us what you're doing, > there's little else to suggest. > > > suggestions to recover the essential information which you would include >> as >> part of methods? >> >> > The .mdp file has all the instructions for the simulation. If you don't > have that around for whatever reason (very bad to get rid of such files!), > all of the same information is recorded in the beginning of the .log file > or can be written out by gmxdump. In the latter case, make sure to > redirect the output to a file rather than just have thousands of lines of > text blur by in the terminal. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Ankita Naithani -- 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] gmxcheck
Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any suggestions to recover the essential information which you would include as part of methods? Kind regards, Ankita On Mon, Nov 4, 2013 at 12:11 PM, Justin Lemkul wrote: > > > On 11/4/13 5:06 AM, Ankita Naithani wrote: > >> Hi, >> >> I was wondering if anyone could help me with the gmxcheck function? In the >> manual it is written, -m flag is given a LaTeX file will be written >> consisting of a rough outline for a methods section for a paper. >> I tried it several times but there isn't any file that I can see. >> >> > You need to provide a .tpr file, as well. > > > I had run some simulations but now that I had to write a quick report >> about >> the parameters and essential things mentioned likewise in the methods >> section, I realized that I had not kept tab of the basic details so found >> out that gmxcheck does that but I haven't been successful. >> >> > The output from gmxcheck will be of little use, in my opinion. All it > does is write some chosen .mdp settings in full sentences, which does not > give you a complete description of all the relevant settings. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Ankita Naithani -- 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] gmxcheck
Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. I had run some simulations but now that I had to write a quick report about the parameters and essential things mentioned likewise in the methods section, I realized that I had not kept tab of the basic details so found out that gmxcheck does that but I haven't been successful. Any insight on this would be quite helpful. Kind regards -- Ankita Naithani -- 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] continuing the terminated simulation
Hi Delara, To continue a crashed simulation you just need to type in the following command without deffnm md. mdrun -s md_0_1.tpr -cpi md_0_1.cpt You can check the link here: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts The continuation is down via the .cpt file. the _prev.cpt is just a backup copy and you need only .cpt file to begin the crashed run. The difference is explained here: http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File Cheers, Ankita On Wed, Oct 30, 2013 at 9:26 AM, delara aghaie wrote: > Dear Gromacs users > Hello, > I use gromacs version 4.5.5. I have started with Lysozime in water > simulation. (Justin tutorials) > The md part of simulation was terminated. Now I want to continue the > simulation from the interruption point. Is this command line correct? > mdrun -deffnm md_0_1 -smd_0_1.tpr -cpi > md_0_1.tpr.cpt??? > > I am not sure whether to use only -cpi md_0_1.tpr.cpt with mdrun command > or both .tpr and .cpt files??? > > another question is that whether continuing the simulation should be done > via file md_0_1.tpr.cpt or md_0_1.tpr_prev.cpt ? and what in the > difference between them? > > Thanks in advance > Regards > D.M > -- > 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 > -- Ankita Naithani -- 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: Covariance file format
Hi Tsjerk, Thank you very much. It was extremely helpful. Kind regards Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > No, the file contains the 3Nx3N covariance matrix, row by row, split over > triplets, mass weighted if you did the analysis mass-weighted. But for > C-alpha only there is no difference between mass-weighted and > non-mass-weighted, except for global scaling. > > Cheers, > > Tsjerk > > > > On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > > > Coffee is always magical, I tell you. Just a sniff in the air and it > makes > > things clear. > > > > So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? > > > > By any chance we don't obtain a file I. Which the first column wud have > > alpha atom one second column would have 2nd aloha atom n third would have > > correlation between them? > > > > > > > > Kind regards, > > > > Ankita > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > Hi Ankita, > > > > > > I should not answer questions before coffee!! Sorry. > > > > > > It's the covariance matrix! So it's > > > > > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > > > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > > > ... > > > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > > > > > Silly me :| > > > > > > Tsjerk > > > > > > > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani < > > ankitanaith...@gmail.com > > > >wrote: > > > > > > > Hi Tsjerk, > > > > Thank you for your reply. So, these are the eigenvectors. By any > > chance, > > > > can we obtain the covariance matrix containing the information of > > residue > > > > fluctuations I.e. the covariance information. Actually, it was needed > > to > > > > obtain the dot plot delta ri dot delta rj so I don't think so I can > use > > > the > > > > eigenvectors > > > > > > > > > > > > Kind regards > > > > > > > > Ankita > > > > > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > > > > > Hi Ankita, > > > > > > > > > > The fie contains the eigenvectors as > > > > > > > > > > x1 y1 z1 > > > > > x2 y2 z2 > > > > > ... > > > > > xN yN zN > > > > > > > > > > Hope it helps, > > > > > > > > > > Tsjerk > > > > > > > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > > > ankitanaith...@gmail.com > > > > > >wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I wanted to know the exact format of covariance.dat file as > > generated > > > > by > > > > > > g_covar during covariance analysis. The file format mentioned in > > the > > > > > manual > > > > > > was not quite clear to understand. I need to use the matrix > > > > information n > > > > > > so needed to know how the data is stored. My matrix is for 1992 > > > calpha > > > > > > atoms. > > > > > > > > > > > > It would be really helpful if someone could explain the file > > format. > > > > > > > > > > > > Kind regards, > > > > > > > > > > > > Ankita > > > > > > > > > > > > > > > > > > -- > > > > > > Ankita Naithani > > > > > > -- > > > > > > 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: Covariance file format
Hi Tsjerk, Coffee is always magical, I tell you. Just a sniff in the air and it makes things clear. So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? By any chance we don't obtain a file I. Which the first column wud have alpha atom one second column would have 2nd aloha atom n third would have correlation between them? Kind regards, Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > I should not answer questions before coffee!! Sorry. > > It's the covariance matrix! So it's > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > ... > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > Silly me :| > > Tsjerk > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > Thank you for your reply. So, these are the eigenvectors. By any chance, > > can we obtain the covariance matrix containing the information of residue > > fluctuations I.e. the covariance information. Actually, it was needed to > > obtain the dot plot delta ri dot delta rj so I don't think so I can use > the > > eigenvectors > > > > > > Kind regards > > > > Ankita > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > Hi Ankita, > > > > > > The fie contains the eigenvectors as > > > > > > x1 y1 z1 > > > x2 y2 z2 > > > ... > > > xN yN zN > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > ankitanaith...@gmail.com > > > >wrote: > > > > > > > Hi, > > > > > > > > I wanted to know the exact format of covariance.dat file as generated > > by > > > > g_covar during covariance analysis. The file format mentioned in the > > > manual > > > > was not quite clear to understand. I need to use the matrix > > information n > > > > so needed to know how the data is stored. My matrix is for 1992 > calpha > > > > atoms. > > > > > > > > It would be really helpful if someone could explain the file format. > > > > > > > > Kind regards, > > > > > > > > Ankita > > > > > > > > > > > > -- > > > > Ankita Naithani > > > > -- > > > > 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 > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > 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 > > > > > > > > > -- > > Ankita Naithani > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- Ankita Naithani -- 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: Covariance file format
Hi Tsjerk, Thank you for your reply. So, these are the eigenvectors. By any chance, can we obtain the covariance matrix containing the information of residue fluctuations I.e. the covariance information. Actually, it was needed to obtain the dot plot delta ri dot delta rj so I don't think so I can use the eigenvectors Kind regards Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > The fie contains the eigenvectors as > > x1 y1 z1 > x2 y2 z2 > ... > xN yN zN > > Hope it helps, > > Tsjerk > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani > > >wrote: > > > Hi, > > > > I wanted to know the exact format of covariance.dat file as generated by > > g_covar during covariance analysis. The file format mentioned in the > manual > > was not quite clear to understand. I need to use the matrix information n > > so needed to know how the data is stored. My matrix is for 1992 calpha > > atoms. > > > > It would be really helpful if someone could explain the file format. > > > > Kind regards, > > > > Ankita > > > > > > -- > > Ankita Naithani > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- Ankita Naithani -- 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] Covariance file format
Hi, I wanted to know the exact format of covariance.dat file as generated by g_covar during covariance analysis. The file format mentioned in the manual was not quite clear to understand. I need to use the matrix information n so needed to know how the data is stored. My matrix is for 1992 calpha atoms. It would be really helpful if someone could explain the file format. Kind regards, Ankita -- Ankita Naithani -- 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] Eigenvector and eigenvalues
Hi Tsjerk, Thank you so much for the helpful insight. It will surely help in clearing some basic concepts about eigenvectors and the projections. Also, since in the end you mentioned about my matrix being derived only from C-alpha atoms which proves a limitation, would you reckon a backbone analysis would be better suited to gain some helpful insight into protein motions (Allosteric transitions, effector signalling??). It would however be intensively complicated to derive for the whole protein considering mine is a tetramer and a huge system. Kind regards, Ankita On Sat, Jun 8, 2013 at 9:18 PM, Tsjerk Wassenaar wrote: > Hi Ankita, > > It is important to use the correct names for things. The projection is the > (scalar) inner product of the configuration (coordinates) with the > eigenvector. This is also named the score of the configuration on the > selected eigenvector. With g_anaeig -proj you get the projection. Each > configuration of a trajectory has a projection, and you can plot them over > time, or plot the projection on one eigenvector against another (-2d). You > can also make a 3D plot of three selected eigenvectors (-3d), which is > written out as a PDB file. The projection is not a structure, and you can't > have a movie of structures. What you can do is extract the structures > corresponding to the extreme projections (-extr). Those are always written > per eigenvector. Since the eigenvectors are uncorrelated, the extremes are > not defined for combinations of them. It is also possible to filter a > trajectory on a set of eigenvectors. That will give a trajectory of > (unphysical) structures, in which the projections on the non-selected > eigenvectors are set to zero. This filtering is a matrix operation, using > the matrix of selected eigenvectors and the corresponding atoms of the > trajectory. Because the matrix of eigenvectors is derived from C-alpha > atoms only in your case, it is not possible to get anything else out of it. > > Hope it helps, > > Tsjerk > > > > On Sat, Jun 8, 2013 at 1:06 PM, Ankita naithani >wrote: > > > Hi Tsjerk, > > > > [I am reposting it since my previous attachment was unable to proceed I > > guess] > > > > Thank you for the reply. I am sorry but I don't have the snapshots with > me > > as my system was formatted and I lost that information. However, I > > performed PCA again on Calpha atoms and this time my matrix is 5976X5976 > > wherein 1992 are my total number of calpha atoms. So, yes indeed I did > > something foolish in the previous case to have got that result. However, > I > > will try to look at it and find my mistake so as to not repeat it again. > > > > I would be really grateful if you could help me with my another naive > > query. I wanted to see the movie of first few eigenvectors as individual > > and also separately. I know I can extract that with the help of g_anaeig > > but as I did PCA on only calpha atoms, all I get in the projection of > first > > eigenvector is the calpha dots. Is there any way, I can visualise the > > projection of whole protein on that particular eigenvector? > > > > Secondly, if I want to see the projection along first 10 eigenvectors and > > last 10 eigenvectors (slow modes and fast modes), how could I proceed > > because when I choose -first 1 -last 10, it gives me individual pdb files > > corresponding to the eigenvectors. > > > > Third, as can be judged by my absolute naivety, I did a 2d projection on > PC > > 1 and PC 2. I can visualise that plot in grace as a 2d plot. An example > > file is appended herein. I know each dot might correspond to a particular > > conformation in the trajectory but I really have no idea as to how to > > interpret the results and draw conclusions from these 2d plots and also > 3d > > pdb projections. Could you please guide me in the right direction to > > understand these 2d plots and infer the significant results? > > > > > > Kind regards, > > > > Ankita > > > > > > On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar > > wrote: > > > > > >> Hi Ankita, > > >> > > >> Please provide the commands you've run and the screen output from > > g_covar. > > >> > > >> Cheers, > > >> > > >> Tsjerk > > >> > > >> > > >> > > >> On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani < > > ankitanaith...@gmail.com > > >> >wrote: > > >> > > >> > Hi, > > >> > > > >> > I wanted to know about the eigenvectors and ei
Fwd: [gmx-users] Eigenvector and eigenvalues
Hi Tsjerk, [I am reposting it since my previous attachment was unable to proceed I guess] Thank you for the reply. I am sorry but I don't have the snapshots with me as my system was formatted and I lost that information. However, I performed PCA again on Calpha atoms and this time my matrix is 5976X5976 wherein 1992 are my total number of calpha atoms. So, yes indeed I did something foolish in the previous case to have got that result. However, I will try to look at it and find my mistake so as to not repeat it again. I would be really grateful if you could help me with my another naive query. I wanted to see the movie of first few eigenvectors as individual and also separately. I know I can extract that with the help of g_anaeig but as I did PCA on only calpha atoms, all I get in the projection of first eigenvector is the calpha dots. Is there any way, I can visualise the projection of whole protein on that particular eigenvector? Secondly, if I want to see the projection along first 10 eigenvectors and last 10 eigenvectors (slow modes and fast modes), how could I proceed because when I choose -first 1 -last 10, it gives me individual pdb files corresponding to the eigenvectors. Third, as can be judged by my absolute naivety, I did a 2d projection on PC 1 and PC 2. I can visualise that plot in grace as a 2d plot. An example file is appended herein. I know each dot might correspond to a particular conformation in the trajectory but I really have no idea as to how to interpret the results and draw conclusions from these 2d plots and also 3d pdb projections. Could you please guide me in the right direction to understand these 2d plots and infer the significant results? Kind regards, Ankita On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar wrote: > >> Hi Ankita, >> >> Please provide the commands you've run and the screen output from g_covar. >> >> Cheers, >> >> Tsjerk >> >> >> >> On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani > >wrote: >> >> > Hi, >> > >> > I wanted to know about the eigenvectors and eigenvalues. I recently >> > performed the principal component analysis (only the backbone into >> > consideration) on a trajectory of 2000 residues. I obtained 15641 >> > eigenvectors and 17928 eigenvalues. There is a difference in the number, >> > which I am not quite sure off (perhaps that has to do with eigenvalue >> for >> > each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I >> > may be wrong completely but since there are 15641 eigenvectors, then >> > shouldn't there by only 15641 eigenvalues for those eigenvectors) >> > >> > My second problem lies that I am trying to extract information or say >> RMSF >> > values for the first 10 eigenvectors (10 slowest modes) and the last 10 >> > eigenvectors (fastest modes) and there I face segmentation fault. I can >> get >> > information on the first 10 but when I try last 10 with the command as >> > follows: >> > >> > g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first >> 15631 >> > >> > [where -first should have the starting eigenvector ] >> > >> > (I choose, 15631 since I want the plot for last 10 but I get >> segmentation >> > fault, which is also to do with the fact that the eigenval.xvg has 17928 >> > values. This number doesn't match and so, maybe the plot is from >> > 15631-17928). This has further confused me about the slowest and fastest >> > modes (and somehow I do need information on the first 10 slowest modes >> and >> > 10 fastest modes). In a broad way, the slowest modes would be the ones >> with >> > high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give >> the >> > slowest 10 modes and the last 10 in eigenval.xvg should give the >> fastest 10 >> > modes. >> > >> > Here, again I feel quite confused because eigenval.xvg has 17928 entries >> > and in the legend, it says that x axis is the eigenvector index and y >> axis >> > is eigenvalue index so it leaves me quite perplexed about the problem. >> > >> > I am sorry for this extremely long and confusing post, but any help in >> this >> > regard would be really beneficial. >> > >> > >> > Kind regards, >> > >> > Ankita >> > >> > -- >> > Ankita Naithani >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Supp
[gmx-users] Eigenvector and eigenvalues
Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed the principal component analysis (only the backbone into consideration) on a trajectory of 2000 residues. I obtained 15641 eigenvectors and 17928 eigenvalues. There is a difference in the number, which I am not quite sure off (perhaps that has to do with eigenvalue for each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I know I may be wrong completely but since there are 15641 eigenvectors, then shouldn't there by only 15641 eigenvalues for those eigenvectors) My second problem lies that I am trying to extract information or say RMSF values for the first 10 eigenvectors (10 slowest modes) and the last 10 eigenvectors (fastest modes) and there I face segmentation fault. I can get information on the first 10 but when I try last 10 with the command as follows: g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg -first 15631 [where -first should have the starting eigenvector ] (I choose, 15631 since I want the plot for last 10 but I get segmentation fault, which is also to do with the fact that the eigenval.xvg has 17928 values. This number doesn't match and so, maybe the plot is from 15631-17928). This has further confused me about the slowest and fastest modes (and somehow I do need information on the first 10 slowest modes and 10 fastest modes). In a broad way, the slowest modes would be the ones with high eigenvalues say, first 10 eigenvectors in eigenval.xvg would give the slowest 10 modes and the last 10 in eigenval.xvg should give the fastest 10 modes. Here, again I feel quite confused because eigenval.xvg has 17928 entries and in the legend, it says that x axis is the eigenvector index and y axis is eigenvalue index so it leaves me quite perplexed about the problem. I am sorry for this extremely long and confusing post, but any help in this regard would be really beneficial. Kind regards, Ankita -- Ankita Naithani -- 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] Snapshot and co-ordinate query
Hi Justin, Thank you so much for the clarification. Kind regards, Ankita On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul wrote: > > > On 6/5/13 3:03 PM, Ankita naithani wrote: > >> Hi, >> >> I have two questions. >> >> I have performed a simulation on my protein structure and after the >> simulation, I used trjconv to obtain snapshots after every 10 ns with the >> following command: >> >> trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb >> >> > This command will produce one snapshot. If you're looking to get multiple > snapshots, it is easier to combine -skip -sep to write out multiple > snapshots in one command. > > > and chose 0 (system) for the group. >> However, when I see the same structure in PyMol as cartoon representation, >> I see the protein structure and few of the residues scattered elsewhere of >> a particular chain, say chain A. I am concerned whether my residues of >> that >> particular chain fragmented during simulation or is my way of obtaining >> snapshots wrong? >> >> > The molecule isn't fragmented, it's just split across periodic boundaries. > trjconv can take care of that too (see trjconv -h). > > Also, there was another question, I wanted to know how the geometry is >> preserved in the average structure as computed by gromacs?The average >> >> structure calculated during analysis would be the average of all the >> atomic >> positions/co-ordinates during the length of simulation. But, I wanted to >> know how are the bond angles treated for computation of the average >> structure? Since, we use the structure for further analysis too. Are the >> bond lengths distorted or they are retained while average is being >> computed? Also, what are the co-ordinates used for this computation? >> >> > http://www.gromacs.org/**Documentation/Terminology/**Average_Structure<http://www.gromacs.org/Documentation/Terminology/Average_Structure> > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Ankita Naithani -- 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] Snapshot and co-ordinate query
Hi, I have two questions. I have performed a simulation on my protein structure and after the simulation, I used trjconv to obtain snapshots after every 10 ns with the following command: trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb and chose 0 (system) for the group. However, when I see the same structure in PyMol as cartoon representation, I see the protein structure and few of the residues scattered elsewhere of a particular chain, say chain A. I am concerned whether my residues of that particular chain fragmented during simulation or is my way of obtaining snapshots wrong? Also, there was another question, I wanted to know how the geometry is preserved in the average structure as computed by gromacs?The average structure calculated during analysis would be the average of all the atomic positions/co-ordinates during the length of simulation. But, I wanted to know how are the bond angles treated for computation of the average structure? Since, we use the structure for further analysis too. Are the bond lengths distorted or they are retained while average is being computed? Also, what are the co-ordinates used for this computation? I would be really grateful if you could kindly guide me towards these queries. Kind regards -- Ankita Naithani -- 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: rmsf analysis
Hi Vansh, md.tpr is the run input file for production md and is generated immediately after issuing the command grompp. So, this is is file which you then use to run the production md using mdrun. On Wed, Mar 13, 2013 at 10:55 AM, vansh wrote: > hello ankita, > I am for sure is in the same directory but as you mentioned about the > name...can you please suggest me at what step does this file is generated??? > > > thanks and regards] > > > > - > thanks in advance :) > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/rmsf-analysis-tp5006285p5006288.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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 -- Ankita Naithani -- 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] rmsf analysis
Hi, It should be able to find md.tpr unless your file is named something else or you are issuing the command from other directory. On Wed, Mar 13, 2013 at 9:31 AM, vansh wrote: > to analyse the flexibility of the protein i used tge command > g_rmsf -s md.tpr -f traj.xtc -oq > > but its showing that - can not open md.tpr file > > as i am new to it cant figure it outany suggestions... > > > > - > thanks in advance :) > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/rmsf-analysis-tp5006285.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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 -- Ankita Naithani -- 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] MM-GB/SA analysis in Gromacs
Hi Andrea, Thank you so much for bringing forth the paper. I have performed a MD simulation and would very much like to use the tool mentioned in the paper to calculate the binding free energy. Is it possible for you to kindly give me an access to the same and also a brief explanation as to how to use the same? My email id is ankitanaitha...@gmail.com Best Wishes Ankita On Thu, Nov 29, 2012 at 12:32 PM, andrea spitaleri wrote: > Dear all, > > I would like to bring to your attention this paper > http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 > in which we made a tool to perform MM/PBSA binding free energy calculation > in automatic fashion, using torque/pbs parallel system implemented in most > clusters. The input of the tools are just the xtc trajectory, the tpr and > eventually the index file. It does perform the computational alanine > scanning (CAS) too. The tool is available upon request. Further details on > the paper. > > > Regards, > > and > > > On 11/29/2012 10:42 AM, Anna Marabotti wrote: >> >> Dear gmx-users, >> >> I ran several MD simulations using Gromacs 4.5.4 version, and now I'd >> need to calculate binding free energies using the MM-GBSA method. I >> searched through the manual and through the gmx-users archive, but I >> didn't find a way to do it. I found an old post in which it appeared >> that in the version 4.5 this possibility would have been available >> (http://lists.gromacs.org/pipermail/gmx-users/2010-July/052302.html), >> but it seems to me that this kind of analysis has not been implemented >> yet. >> In another more recent post, I see that somebody has used mdrun -rerun >> in order to perform calculations, but I don't understand the correct >> procedure to use (apart from the suggestion of using .trr instead of >> .xtc files in order to avoid errors). >> >> Does anyone have suggestions in order to do this analysis with Gromacs >> trajectories, before I make these calculations with another program? >> >> Many thanks in advance and best regards >> Anna >> > > -- > - > Andrea Spitaleri PhD > Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele > Centro di Genomica Traslazione e Bioinformatica > Biomolecular NMR Laboratory Dibit2 Basilica 3A2 > Via Olgettina 58 > 20132 Milano > Italy > Tel: 0039-0226434348 > Fax: 0039-0226434153 > http://sites.google.com/site/andreaspitaleri/ > http://www.linkedin.com/in/andreaspitaleri > - > > -- > 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 -- Ankita Naithani -- 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: Continuing a simulation plus another error
Hi Justin, Thank you so much for your response. I also noticed that when I type in gmxcheck -f md.cpt to see which version was used, I get the same fatal error of "Attempting to read a checkpoint file of version 13 with code of version 12". In my linux machine, the gromacs version is 4.5.5 and the one on the cluster is also 4.5.5. I just offloaded the data from the cluster and was trying to run the test for continuing simulation before submitting it to the cluster for continuation. Could you please suggest me something in this regard too. I understand that the versions would be different but my system and cluster have the same version of gromacs. Also, is version 13 being used by gromacs 4.6? In that case, how do we continue a simulation with that version? If somehow someone updated the software or switched it to gromacs 4.6 in the cluster, I will then directly invoke mdrun there but I would need to know if the command would be the same for continuing the simulation in gromacs 4.6? i.e. mdrun -cpi md.cpt -s md.tpr Sorry for bothering with silly questions, my time on the cluster runs out in 2 days so I really could do with as much help I can for now On Mon, Dec 24, 2012 at 5:28 PM, Justin Lemkul wrote: > > > On 12/24/12 11:54 AM, Ankita naithani wrote: >> >> Hi again, >> >> Sorry for the repetition in email. >> >> When I ran the mdrun command, I got an error of >> >> "Attempting to read a checkpoint file of version 13 with code of version >> 12" >> >> Can anyone please help me with this error too? >> > > This means you are not using the same version of the code as the previous > run. > > >> On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani >> wrote: >>> >>> Hi, >>> >>> I am running a protein simulation for 70 ns. I had a MPI run but due >>> to my time constraints on the server, it stopped after 28ns. Now, I >>> want to continue the simulation from the same point up until I use up >>> my server time. >>> >>> I just wanted to confirm that there are two checkpoint files written, >>> md.cpt and md_prev.cpt. It would be really helpful if anyone could >>> advice as to which file would be better to choose to continue the >>> simulation? >>> > > Checkpoint files are written every 15 minutes by default and the names are > recycled between (prefix).cpt and (prefix)_prev.cpt to indicate the most > recently saved state and the previous one. Either can be used for > continuing the stopped run, but the current state is most advantageous to > avoid wasted time. The previous state is saved as a backup in case of a > corrupted checkpoint file or frame in the trajectory that would require > starting from a previous point. > > >>> Also, I wanted a confirmation that if I use: >>> >>> mdrun -s topol.tpr -cpi md.cpt -append >>> >>> Do I also need to add -deffnm md? >>> > > That depends entirely upon the file names present and what the original > invocation of mdrun was. > > >>> and if I run mdrun, would it then continue from say 28ns and up until >>> the time specified in the .mdp file? The reason I wanted to confirm >>> this is that before submitting it to the server, I ran it in my local >>> machine and when I see the log file, it shows step 0 and Time 0., >>> does that mean it is starting the simulation from scratch because I >>> had expected it to show me step from wherever it exited last and >>> continue from there on. >>> > > The run will start from scratch if for some reason the checkpoint file > cannot be found or read for whatever reason. If you are trying to run on a > local machine with a different number of processors, for instance, the > checkpoint state will not be the same so the run will start over again. > > Note that most of this information is online for quick reference: > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x > > -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 -- Ankita Naithani -- 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: Continuing a simulation plus another error
Hi again, Sorry for the repetition in email. When I ran the mdrun command, I got an error of "Attempting to read a checkpoint file of version 13 with code of version 12" Can anyone please help me with this error too? On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani wrote: > Hi, > > I am running a protein simulation for 70 ns. I had a MPI run but due > to my time constraints on the server, it stopped after 28ns. Now, I > want to continue the simulation from the same point up until I use up > my server time. > > I just wanted to confirm that there are two checkpoint files written, > md.cpt and md_prev.cpt. It would be really helpful if anyone could > advice as to which file would be better to choose to continue the > simulation? > > Also, I wanted a confirmation that if I use: > > mdrun -s topol.tpr -cpi md.cpt -append > > Do I also need to add -deffnm md? > > and if I run mdrun, would it then continue from say 28ns and up until > the time specified in the .mdp file? The reason I wanted to confirm > this is that before submitting it to the server, I ran it in my local > machine and when I see the log file, it shows step 0 and Time 0., > does that mean it is starting the simulation from scratch because I > had expected it to show me step from wherever it exited last and > continue from there on. > > Would really appreciate if anyone could guide me further. > > -- > Ankita Naithani -- Ankita Naithani -- 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] Continuing a simulation
Hi, I am running a protein simulation for 70 ns. I had a MPI run but due to my time constraints on the server, it stopped after 28ns. Now, I want to continue the simulation from the same point up until I use up my server time. I just wanted to confirm that there are two checkpoint files written, md.cpt and md_prev.cpt. It would be really helpful if anyone could advice as to which file would be better to choose to continue the simulation? Also, I wanted a confirmation that if I use: mdrun -s topol.tpr -cpi md.cpt -append Do I also need to add -deffnm md? and if I run mdrun, would it then continue from say 28ns and up until the time specified in the .mdp file? The reason I wanted to confirm this is that before submitting it to the server, I ran it in my local machine and when I see the log file, it shows step 0 and Time 0., does that mean it is starting the simulation from scratch because I had expected it to show me step from wherever it exited last and continue from there on. Would really appreciate if anyone could guide me further. -- Ankita Naithani -- 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] TIP4P water model
Hi, So the commands from the beginning are appended below: pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro (I choose option 6 for AMBER99sb-ILDN force field and then option 2 for TIP4P water model) editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron genbox -cp system_box.gro -cs tip4p.gro -o system_solv.gro -p topol.top grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr And it is here that I get the error : Fatal error: number of coordinates in coordinate file (system_solv.gro, 421880) does not match topology (topol.top, 416008) I am appending below the contents of my topology file: ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Sep 21 14:02:35 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.5 ; ; Command line was: ; /usr/local/src/gromacs/bin/pdb2gmx_d -vsite h -f 3HQN_tet-nolig.pdb -o system.gro ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_A2.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_B2.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_C2.itp" #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_D2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip4p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A2 1 Protein_chain_B 1 Protein_chain_B2 1 Protein_chain_C 1 Protein_chain_C2 1 Protein_chain_D 1 Protein_chain_D2 1 SOL 340 SOL 394 SOL 340 SOL 394 SOL 94333 --- I cannot understand as to why it is generating error at this stage. It would be really helpful if you could advice me how to proceed from here. Best Wishes, Ankita On Sat, Sep 22, 2012 at 12:57 AM, Justin Lemkul wrote: > > > On 9/21/12 7:55 PM, Peter C. Lai wrote: >> >> Perhaps genion is not removing the dummy atoms properly? >> > > The problem is occurring with grompp before genion. We would need to see > all the prior commands (exactly copied and pasted from the terminal) as well > as the [molecules] section of the topology, to at least start to guess at > what's wrong. It is unusual to find a failure in grompp before genion. > > -Justin > > >> On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote: >>> >>> Hi all, >>> >>> I am trying to begin a simulation of a protein. >>> >>> I am using AMBER99sb-ILDN force field and TIP4P water model. However, >>> I am facing a problem in the ion adding step. >>> >>> when I issue the grompp command to generate the necessary .tpr file >>> for simulation to be utilised by genion tool, I get the following >>> error : >>> >>> "Fatal error: >>> number of coordinates in coordinate file (system_solv.gro, 421880) >>> does not match topology (topol.top, 416008) >>> " >>> >>> However, I have rechecked several times my topology file and the >>> co-ordinate file and I am running it pretty straightforward to get >>> this error. When I try TIP3P water model for the same protein, I do >>> not get the error. >>> >>> I get the same error when I use TIP4P-Ew water model too. I have >>> decide a better water model for my system before I run my final >>> production simulations and so I have been trying to compare both the >>> water models. I am wondering if anyone could kindly suggest the >>> possible reason for this error because ideally, it should not be >>> giving me any error at this stage as I haven't manipulated with >>> anything. >>> >>> I am also appending my ions.mdp info below: >>> >>> ; ions.mdp - used as input into grompp to generate ions.tpr >>> ; Parameters describing what to do, when to stop and what to save >>> integrator = steep ; Algorithm (steep = steepest descent >>> minimization) >>> emtol = 1000.0; Stop mini
Re: [gmx-users] g_confrms
Hi Mark, I haven't been able to figure out the reason of the difference between the two structures. When I prompt for my backbone to be fitted against each other, the initial structure has 2965 elements and the final output file has 2955 elements. Could you please suggest the possible reason for the difference? On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham wrote: > On 16/09/2012 11:49 PM, Ankita naithani wrote: >> >> Hi, >> >> I am trying to use g_confrms to compare my initial and final structure >> and fit them on their backbone. However, I notice a difference of 10 >> atoms in both of these structures and so I am unable to use g_confrms. >> Can anyone please help me and advice me regarding this as the manual >> does mention about using g_confrms irrespective of the number of >> atoms. > > > Why are the two things you are trying to compare not the same? > > 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 -- Ankita Naithani -- 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] g_confrms
Hi, I am trying to use g_confrms to compare my initial and final structure and fit them on their backbone. However, I notice a difference of 10 atoms in both of these structures and so I am unable to use g_confrms. Can anyone please help me and advice me regarding this as the manual does mention about using g_confrms irrespective of the number of atoms. Best Wishes, -- Ankita Naithani -- 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] NPT Equilibration error
Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure. However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain decomposition steps. Fatal error: 8 particles communicated to PME node 1 are more than 2/3 times the cut off out of the domain decomposition cell of their charge group in dimension X. My npt.mdp files looks like follows: title = NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 125000; 250 ps dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 5 ps nstvout = 0 ; save velocities every 5 ps nstenergy = 10; save energies every 5 ps nstlog = 1000 ; update log file every 5 ps ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10; 50 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = berendsen ; Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 318 318 ; reference temperature, one for each group, in K nsttcouple = 0.; 1 by default ; Pressure coupling is off pcoupl = berendsen ; Berendsen thermostat pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Could you please guide me to solve the problem? -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Topology file
Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani wrote: > Hi, > > I noticed that in my topology file, there is no inclusion of position > restraint file for my protein. For instance, my topology file looks > like this: > > ; Include forcefield parameters > #include "gromos53a6.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_E.itp" > #include "topol_Protein_chain_F.itp" > #include "topol_Protein_chain_G.itp" > > ;Include ligand topology > #include "FDP_Dp.itp" > > ; Include water topology > #include "gromos53a6.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include topology for ions > #include "gromos53a6.ff/ions.itp" > > > But, after running pdb2gmx, I do get 4 posre files for all the > individual chains. Do I need to add in them manually? Also, I am > unable to understand as to why did it not get included in the first > instance itself? I am using gromos53a6 force field. > > > Best Wishes, > > -- > Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Topology file
Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_E.itp" #include "topol_Protein_chain_F.itp" #include "topol_Protein_chain_G.itp" ;Include ligand topology #include "FDP_Dp.itp" ; Include water topology #include "gromos53a6.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ions topology
Dear Mark, Thank you for your reply. I am using gromos53a6 force field. On Tue, Aug 14, 2012 at 11:16 AM, Mark Abraham wrote: > On 14/08/2012 7:45 PM, Ankita naithani wrote: >> >> Dear All, >> >> I wanted to ask that from where can I get the topologies and >> co-ordinate information for Mg and K ions? For the ligands, I could >> get it from PRODRG software as suggested in the tutorial but my >> protein needs the crucial ions Mg and K before I can begin with my >> simulations. > > > Availability depends on the force field, so start looking in its files > distributed by GROMACS. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Ions topology
Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before I can begin with my simulations. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein-ligand - genion error
Hi Justin, Thank you so much for your reply. It really helped me a lot. I think I have managed to clear this step. Thanks once again. Best Wishes, On Fri, Aug 10, 2012 at 6:30 PM, Justin Lemkul wrote: > > > On 8/10/12 1:26 PM, Ankita naithani wrote: >> >> Hi Justin, >> >> Thank you for your response. >> >> The co-ordinate file that you have mentioned. Is it the one obtained >> after running pdb2gmx step or the one after running genbox step? >> >> Also, I am putting few outputs for your referral.. >> >> My co-ordinate file after building topology and incorporating my >> ligand topology, looks like this: >> >> >> 498GLU O119587 0.147 1.260 4.509 >>498GLU O219588 0.017 1.177 4.669 >>501HOH OW19589 -3.995 3.677 -0.161 >> >> 2139HOHHW223341 0.013 0.653 1.232 >> 1FDP O1P 1 -0.608 6.909 -0.874 >> 1FDP P1 2 -0.474 6.859 -0.904 >> - >> 1FDP O4P 23 0.758 0.467 2.079 >> 1ATP O1G 1 -3.672 4.724 -0.730 >> 1ATP PG 2 -3.697 4.678 -0.871 >> --- >> 1ATP H62 36 3.986 0.936 1.930 >> 1ATP H61 37 4.112 0.822 1.964 >> 1OXL O1 1 -3.442 4.377 -0.541 >> 1OXL C1 2 -3.431 4.424 -0.655 >> >> My co-ordinate file after defining box looks like this: >> >> 498GLU C19586 12.309 9.794 8.852 >>498GLU O119587 12.411 9.858 8.823 >>498GLU O219588 12.281 9.775 8.983 >>501HOH OW19589 8.269 12.275 4.153 >>501HOHHW119590 8.351 12.275 4.210 >>501HOHHW219591 8.187 12.275 4.210 >>503HOH OW19592 10.623 12.907 4.675 >> >> 2139HOHHW123340 12.195 9.170 5.661 >> 2139HOHHW223341 12.277 9.251 5.546 >> 1FDPO1P23342 11.656 15.507 3.440 >> 1FDP P123343 11.790 15.457 3.410 >> 1FDPO2P23344 11.857 15.521 3.280 >> >> >> My co-ordinate file after solvation looks like this: >> >> 498GLUOE219585 11.824 9.468 8.693 >>498GLU C19586 12.309 9.794 8.852 >>498GLU O119587 12.411 9.858 8.823 >>498GLU O219588 12.281 9.775 8.983 >>501HOH OW19589 8.269 12.275 4.153 >>501HOHHW119590 8.351 12.275 4.210 >> -- >> 2139HOHHW223341 12.277 9.251 5.546 >> 1FDPO1P23342 11.656 15.507 3.440 >> 1FDP P123343 11.790 15.457 3.410 >> >> >> 1FDP O423604 15.520 10.331 5.622 >> 1FDP O223605 15.614 10.234 5.451 >> 2SOL OW23606 0.230 0.628 0.113 >> 2SOLHW123607 0.137 0.626 0.150 >> 2SOLHW223608 0.231 0.589 0.021 >> 3SOL OW23609 0.569 1.275 1.165 >> 3SOLHW123610 0.476 1.268 1.128 >> 3SOLHW223611 0.580 1.364 1.209 >> 4SOL OW23612 1.555 1.511 0.703 >> - >> >> 91503SOLHW198110 16.284 14.907 11.256 >> 91503SOLHW298111 16.159 14.910 11.360 >> 91504SOL OW98112 14.935 15.974 11.472 >> 91504SOLHW198113 15.034 15.963 11.463 >> 91504SOLHW298114 14.895 15.888 11.504 >> >> -- >> >> and my topology file has following: >> >> [ molecules ] >> ; Compound#mols >> Protein_chain_A 1 >> Protein_chain_B 1 >> Protein_chain_C 1 >> Protein_chain_D 1 >> SOL 167 >> SOL 379 >> SOL 305 >> SOL 400 >> FDP 4 >> ATP 4 >> OXL 4 >> SOL 91503 >> >> >> I think you are talking about the co-ordinate file obtained after >> solvation, right? >> > > Yes. > > >> I do notice that FDp is between HOH and SOL but if I remove FDP, my >> ligand will be removed. >> > > I didn't say to remove it, I said to change its position within the > coordinate file. Right now, you have FDP, ATP, and OXL breaking up your SOL > section. You can't do that - all the SOL entries need to be continuous in > the coordinate and topology files. > > >> The second thing I noticed is that I had put the information for all >> the three ligands i.e. FDP,ATP and OXL but subsequently, I find that >> only FDP is present in these files and not ATP and OXL. >
Re: [gmx-users] Protein-ligand - genion error
Hi Justin, Thank you for your response. The co-ordinate file that you have mentioned. Is it the one obtained after running pdb2gmx step or the one after running genbox step? Also, I am putting few outputs for your referral.. My co-ordinate file after building topology and incorporating my ligand topology, looks like this: 498GLU O119587 0.147 1.260 4.509 498GLU O219588 0.017 1.177 4.669 501HOH OW19589 -3.995 3.677 -0.161 2139HOHHW223341 0.013 0.653 1.232 1FDP O1P 1 -0.608 6.909 -0.874 1FDP P1 2 -0.474 6.859 -0.904 - 1FDP O4P 23 0.758 0.467 2.079 1ATP O1G 1 -3.672 4.724 -0.730 1ATP PG 2 -3.697 4.678 -0.871 --- 1ATP H62 36 3.986 0.936 1.930 1ATP H61 37 4.112 0.822 1.964 1OXL O1 1 -3.442 4.377 -0.541 1OXL C1 2 -3.431 4.424 -0.655 My co-ordinate file after defining box looks like this: 498GLU C19586 12.309 9.794 8.852 498GLU O119587 12.411 9.858 8.823 498GLU O219588 12.281 9.775 8.983 501HOH OW19589 8.269 12.275 4.153 501HOHHW119590 8.351 12.275 4.210 501HOHHW219591 8.187 12.275 4.210 503HOH OW19592 10.623 12.907 4.675 2139HOHHW123340 12.195 9.170 5.661 2139HOHHW223341 12.277 9.251 5.546 1FDPO1P23342 11.656 15.507 3.440 1FDP P123343 11.790 15.457 3.410 1FDPO2P23344 11.857 15.521 3.280 My co-ordinate file after solvation looks like this: 498GLUOE219585 11.824 9.468 8.693 498GLU C19586 12.309 9.794 8.852 498GLU O119587 12.411 9.858 8.823 498GLU O219588 12.281 9.775 8.983 501HOH OW19589 8.269 12.275 4.153 501HOHHW119590 8.351 12.275 4.210 -- 2139HOHHW223341 12.277 9.251 5.546 1FDPO1P23342 11.656 15.507 3.440 1FDP P123343 11.790 15.457 3.410 1FDP O423604 15.520 10.331 5.622 1FDP O223605 15.614 10.234 5.451 2SOL OW23606 0.230 0.628 0.113 2SOLHW123607 0.137 0.626 0.150 2SOLHW223608 0.231 0.589 0.021 3SOL OW23609 0.569 1.275 1.165 3SOLHW123610 0.476 1.268 1.128 3SOLHW223611 0.580 1.364 1.209 4SOL OW23612 1.555 1.511 0.703 - 91503SOLHW198110 16.284 14.907 11.256 91503SOLHW298111 16.159 14.910 11.360 91504SOL OW98112 14.935 15.974 11.472 91504SOLHW198113 15.034 15.963 11.463 91504SOLHW298114 14.895 15.888 11.504 -- and my topology file has following: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 Protein_chain_D 1 SOL 167 SOL 379 SOL 305 SOL 400 FDP 4 ATP 4 OXL 4 SOL 91503 I think you are talking about the co-ordinate file obtained after solvation, right? I do notice that FDp is between HOH and SOL but if I remove FDP, my ligand will be removed. The second thing I noticed is that I had put the information for all the three ligands i.e. FDP,ATP and OXL but subsequently, I find that only FDP is present in these files and not ATP and OXL. Please, could help me with both my problems. On Fri, Aug 10, 2012 at 6:08 PM, Justin Lemkul wrote: > > > On 8/10/12 1:05 PM, Ankita naithani wrote: >> >> Dear All, >> >> I have been trying to perform simulation for a Protein and Ligand >> complex. However, when I run genion, I get an error "The solvent group >> SOL is not continuous: index[37530=23341, index[3754]=23606. >> >> I remember reading someone posting a similar problem and the solution >> was provided, according to which we need to manipulate the co-ordinate >> file and topology file. But, the problem is I really cannot understand >> at the moment as to what exactly changes I should make in order to run >> it and rectify this error. I would be really grateful if someone >> could help me and let me know as to what exactly and how I need to >> incorporate the changes. Also, the co-ordinate file, should the >> changes be made to the one obtained after running the genbox step? >> > > In the coordinate file, you'll find lines for SOL, then something else, then > more SOL. Your SOL lines need to be continuous, so you have to cut out > whatever is breaking the two solvent blocks, put it either before or after > SOL, and then make sure the [molecules] section of the topology agrees with > contents of the new coordinate file in terms of number of molecules and > order of appearance. > > -Justin > > -- > >
[gmx-users] Protein-ligand - genion error
Dear All, I have been trying to perform simulation for a Protein and Ligand complex. However, when I run genion, I get an error "The solvent group SOL is not continuous: index[37530=23341, index[3754]=23606. I remember reading someone posting a similar problem and the solution was provided, according to which we need to manipulate the co-ordinate file and topology file. But, the problem is I really cannot understand at the moment as to what exactly changes I should make in order to run it and rectify this error. I would be really grateful if someone could help me and let me know as to what exactly and how I need to incorporate the changes. Also, the co-ordinate file, should the changes be made to the one obtained after running the genbox step? Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein - Ligand tetramer simulation
Hi Justin, Thank you so much for a swift response. I will try as suggested and get back to you with my hurdles. Appreciate the help! Best Wishes, Ankita On Thu, Aug 9, 2012 at 4:09 PM, Justin Lemkul wrote: > > > On 8/9/12 10:40 AM, Ankita naithani wrote: >> >> Hi all, >> >> I am trying to put a tetrameric protein for Energy Minimization to be >> followed by MD simulation of course. But, my problem is that it is a >> tetramer and also I need to perform the simulation with the ligand. I >> have read the tutorial for Protein-Ligand simulation but that explains >> for only one chain, whereas I am talking about 4 chains here. >> I need to put in my tetramer with ligands attached for simulations. >> If I have understood correctly, the tutorial mentions about extracting >> the ligand from PDB and then copying the PDB file of the extracted >> ligand into PRODRG and then retrieving the topology file from there >> and appending it to the topology output of the protein without ligands >> attached. But this is specific for one chain i.e. the PDB co-ordinate >> given to PRODRG is for the ligand from one chain. > > > Yes, and you would have to acquire properly processed coordinates for each > copy of the ligand. You only need one .itp file (which in theory should be > the same, regardless of which copy of the ligand you input to PRODRG), but > you need coordinate files for the four copies of the ligands from each > chain. These would then be appended to the processed protein coordinate > file in the same manner as the tutorial suggests. > > PRODRG topologies require significant modification to be considered viable > for real simulation use. See hints in the tutorial and associated > publications. > > >> The second question is that can I not submit the whole protein-ligand >> complex to GROMACS and then run pdb2gmx for generating topology. How >> do I go about that? I understand that I would have to change the top >> directories of GROMACS to accommodate my ligands but I don't know how >> to do that. >> > > Run pdb2gmx on the protein only, then append ligand coordinates as suggested > above. > > -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 > * Only plain text messages are allowed! > * 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 -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein - Ligand tetramer simulation
Hi all, I am trying to put a tetrameric protein for Energy Minimization to be followed by MD simulation of course. But, my problem is that it is a tetramer and also I need to perform the simulation with the ligand. I have read the tutorial for Protein-Ligand simulation but that explains for only one chain, whereas I am talking about 4 chains here. I need to put in my tetramer with ligands attached for simulations. If I have understood correctly, the tutorial mentions about extracting the ligand from PDB and then copying the PDB file of the extracted ligand into PRODRG and then retrieving the topology file from there and appending it to the topology output of the protein without ligands attached. But this is specific for one chain i.e. the PDB co-ordinate given to PRODRG is for the ligand from one chain. The second question is that can I not submit the whole protein-ligand complex to GROMACS and then run pdb2gmx for generating topology. How do I go about that? I understand that I would have to change the top directories of GROMACS to accommodate my ligands but I don't know how to do that. I know my question might be really silly but I am short of time at the moment and would really appreciate any help in this matter. Best Wishes, -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
