Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi, Can somebody please help with WHAM reweighting scheme for REMD analysis. The command "gmx wham" works for Umbrella sampling simulation but I couldnt find a way out for T-REMD. There are similar questions which have been posted here but unfortunately, I haven't found answers for the same. WHAM for REMD has been well documented for AMBER but I couldnt find any help for Gromacs. I am a novice in the field and help is appreciated. Thanks! Nisha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding groups making by make_ndx
Hello Sir, I want to make a new group that contain 2-3 amino acid residues present in protein. But when I am running nvt simulation with this new group error message like multiple t-coupling groups in (1 and 3). So, I am using "splitres" option in make_ndx module of gromacs to separate number of residues in protein. Is there any way to combine these separated residues to make a new group . Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi, There's nothing in GROMACS that specifically supports reweighting replica-exchange simulations. Mark On 03/04/2015 10:03 am, "NISHA Prakash" wrote: > Hi, > > Can somebody please help with WHAM reweighting scheme for REMD analysis. > The command "gmx wham" works for Umbrella sampling simulation but I couldnt > find a way out for T-REMD. > There are similar questions which have been posted here but unfortunately, > I haven't found answers for the same. > WHAM for REMD has been well documented for AMBER but I couldnt find any > help for Gromacs. > I am a novice in the field and help is appreciated. > > Thanks! > > Nisha > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding groups making by make_ndx
Yes, you can combine groups in make_ndx, probably with '&&' or something. Check out its built-in help. Mark On 03/04/2015 10:49 am, "neha chaudhary" wrote: > Hello Sir, > > I want to make a new group that contain 2-3 amino acid residues present in > protein. But when I am running nvt simulation with this new group error > message like multiple t-coupling groups in (1 and 3). So, I am using > "splitres" option in make_ndx module of gromacs to separate number of > residues in protein. Is there any way to combine these separated residues > to make a new group . > > Best Regards, > > *Neha* > > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Life Sciences, > Central University of Himachal Pradesh, > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi Mark, Thanks for your quick response. Can you please suggest a way out? As you pointed out previously, I have 18 ensembles and I would like to study the conformational changes, the interactions between the protein and the ligand and finally, I would like to extract the stable conformation from the simulation data. How do I go about analysing the REMD results. Your tutorial was indeed very helpful but apart from that, I couldn't find much information in that area. Thanks again, Nisha On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham wrote: > Hi, > > There's nothing in GROMACS that specifically supports reweighting > replica-exchange simulations. > > Mark > On 03/04/2015 10:03 am, "NISHA Prakash" wrote: > > > Hi, > > > > Can somebody please help with WHAM reweighting scheme for REMD analysis. > > The command "gmx wham" works for Umbrella sampling simulation but I > couldnt > > find a way out for T-REMD. > > There are similar questions which have been posted here but > unfortunately, > > I haven't found answers for the same. > > WHAM for REMD has been well documented for AMBER but I couldnt find any > > help for Gromacs. > > I am a novice in the field and help is appreciated. > > > > Thanks! > > > > Nisha > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DSSP with gmx 5.0.4
On 03/04/2015 7:36 am, "RJ" wrote: > > Dear gmx users, > > > I tried DSSP of both binary and .exe by renaming it as dssp (dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in usr/local/bin/dssp. Don't try to install a Windows program. Remove everything and then use only the Linux version that matches your system. > > set the excusable too ( "which dssp" /usr/local/bin/dssp). > > > Both of them gives same error as follows; > I also given a permission for dssp file "chmod 777 dssp" but still the error doesnt go. I use all new version but cant fix it? Any help plz. That command can only work if you are in the same directory, and as root. You didn't specify anything about that, so probably the dash binary has the wrong permissions. Inspect them with ls -l. Mark > > gmx do_dssp -f prd_noPBC.xtc -s prd.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2 > > > Selected 5: 'MainChain' > There are 1446 residues in your selected group > dssp cmd='/usr/local/bin/dssp -i ddiyE5RC -o ddPnxMzu > /dev/null 2> /dev/null' > Reading frame 0 time0.000 > Back Off! I just backed up ddiyE5RC to ./#ddiyE5RC.1# > > > --- > Program gmx, VERSION 5.0.4 > Source code file: /home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670 > > > Fatal error: > Failed to execute command: Try specifying your dssp version with the -ver option. > --- > Program gmx, VERSION 5.0.4 > Source code file: /home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670 > > > Fatal error: > Failed to execute command: Try specifying your dssp version with the -ver option. > > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Hi, Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you. Mark On 03/04/2015 7:03 am, "Alex" wrote: > I'm fully aware that this is a forum for discussing Gromacs, but there's > a bit of a frustrating situation that involves using it. > > I need a linear ssDNA chain, sequence of my choosing, anything that will > work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields > for it, everything as is. You suggested AMBER in the past, so AMBER it is. > > > ChemOffice produced a PDB with incompatible atom types. make-na server ( > http://structure.usc.edu/make-na/server.html) also produced something > pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a > usable topology out of the box with an established potential implemented in > Gromacs? Anything that will not involve manual modification of PDBs or > writing text-processing scripts will make me very happy. > > > I will really appreciate any suggestions. > > > Thank you, > > > Alex > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] G_rmsf, reference structure
Dears, I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5. My question is how the RMSF is calculated: A) 1) fitting of the trajectory to the tpr file supplied by -s 2) calculating the averaged atom coordinates over time (x~) 3) calculating the deviation from the averaged structure (x-x~), for each time frame 4) averaging over all time frames OR B) 1) fitting of the trajectory to the tpr file supplied by -s 2) calculating the deviation from the TPR structure (x-x*), for each time frame 3) averaging over all time frames This question has already popped up multiple times in the mailing list: https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html and http://comments.gmane.org/gmane.science.biology.gromacs.user/38359 The problem is that there are multiple answers given: In the first one, it is argued that method A is used in the second mailing list, Marc Abraham states that method B is being used, while Tsjerk mentions method A. I tried to resolve this by looking into thee source code, and although to me it seems that it is option, B, I do not trust my Gromacs code reading capabilities that well ;) Happy Easter! Floris -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] G_rmsf, reference structure
Hi Floris, By default it's A. There is an option for doing B. But B makes no sense. Cheers, Tsjerk On Apr 3, 2015 1:10 PM, "Eerden, van, F.J." wrote: > Dears, > > I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5. > > My question is how the RMSF is calculated: > A) > 1) fitting of the trajectory to the tpr file supplied by -s > 2) calculating the averaged atom coordinates over time (x~) > 3) calculating the deviation from the averaged structure (x-x~), for each > time frame > 4) averaging over all time frames > > OR > B) > 1) fitting of the trajectory to the tpr file supplied by -s > 2) calculating the deviation from the TPR structure (x-x*), for each time > frame > 3) averaging over all time frames > > This question has already popped up multiple times in the mailing list: > https://www.mail-archive.com/gmx-users@gromacs.org/msg25391.html > and > http://comments.gmane.org/gmane.science.biology.gromacs.user/38359 > > The problem is that there are multiple answers given: > In the first one, it is argued that method A is used > in the second mailing list, Marc Abraham states that method B is being > used, while Tsjerk mentions method A. > > I tried to resolve this by looking into thee source code, > and although to me it seems that it is option, B, I do not trust my Gromacs > code reading capabilities that well ;) > > Happy Easter! > > Floris > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Mark, Not to troll, but why did you assume that I didn't do my due diligence before posting here? Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting. Alex > Hi, Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you. Mark On 03/04/2015 7:03 am, "Alex"wrote: I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it. I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is. ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy. I will really appreciate any suggestions. Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Hi Alex, You've solved the issue of getting a DNA structure, but now you're facing a problem of getting Gromacs to prune it. That has to do with the naming scheme mainly. Your best bet is using sed to do name substitution. Probably google will give some good hints about such substitutions in PDB files. Cheers, Tsjerk On Apr 3, 2015 3:40 PM, "Alex" wrote: > Mark, > > > Not to troll, but why did you assume that I didn't do my due diligence > before posting here? > > Because, you see, you could have left that second part of your reply > (which only confirms the legitimacy of my initial question), and it would > make it less insulting. > > > Alex > > > > > > > Hi, > > Googling things like "gromacs DNA structure" is a good bet. There are no > fully standardised naming schemes or workflows, so you will likely not have > something do everything for you. > > Mark > > On 03/04/2015 7:03 am, "Alex" wrote: > > > I'm fully aware that this is a forum for discussing Gromacs, but there's a > bit of a frustrating situation that involves using it. > > I need a linear ssDNA chain, sequence of my choosing, anything that will > work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields > for it, everything as is. You suggested AMBER in the past, so AMBER it is. > > > ChemOffice produced a PDB with incompatible atom types. make-na server ( > http://structure.usc.edu/make-na/server.html) also produced something > pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a > usable topology out of the box with an established potential implemented in > Gromacs? Anything that will not involve manual modification of PDBs or > writing text-processing scripts will make me very happy. > > > I will really appreciate any suggestions. > > > Thank you, > > > Alex > > > > > -- > > Gromacs Users mailing list > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > Best regards, > > Alexmailto:nedoma...@gmail.com > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Hi, I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation. Mark On 03/04/2015 3:40 pm, "Alex" wrote: > Mark, > > > Not to troll, but why did you assume that I didn't do my due diligence > before posting here? > > Because, you see, you could have left that second part of your reply > (which only confirms the legitimacy of my initial question), and it would > make it less insulting. > > > Alex > > > > > > > Hi, > > Googling things like "gromacs DNA structure" is a good bet. There are no > fully standardised naming schemes or workflows, so you will likely not have > something do everything for you. > > Mark > > On 03/04/2015 7:03 am, "Alex" wrote: > > > I'm fully aware that this is a forum for discussing Gromacs, but there's a > bit of a frustrating situation that involves using it. > > I need a linear ssDNA chain, sequence of my choosing, anything that will > work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields > for it, everything as is. You suggested AMBER in the past, so AMBER it is. > > > ChemOffice produced a PDB with incompatible atom types. make-na server ( > http://structure.usc.edu/make-na/server.html) also produced something > pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a > usable topology out of the box with an established potential implemented in > Gromacs? Anything that will not involve manual modification of PDBs or > writing text-processing scripts will make me very happy. > > > I will really appreciate any suggestions. > > > Thank you, > > > Alex > > > > > -- > > Gromacs Users mailing list > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > Best regards, > > Alexmailto:nedoma...@gmail.com > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi, You seem to be essentially asking for your experiment to be designed for you, after an arbitrary simulation is complete. You should think about what and how to observe before you simulate, e.g. from what others have done for similar systems. Consideration of reweighting is secondary. Generally, the only difference with REMD simulations is that you cannot assume that the set of frames from an ensemble are from a contiguous trajectory. Mark On 03/04/2015 11:21 am, "NISHA Prakash" wrote: > Hi Mark, > > Thanks for your quick response. > Can you please suggest a way out? > As you pointed out previously, I have 18 ensembles and I would like to > study the conformational changes, the interactions between the protein and > the ligand and finally, I would like to extract the stable conformation > from the simulation data. > How do I go about analysing the REMD results. > Your tutorial was indeed very helpful but apart from that, I couldn't find > much information in that area. > > Thanks again, > Nisha > > On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham > wrote: > > > Hi, > > > > There's nothing in GROMACS that specifically supports reweighting > > replica-exchange simulations. > > > > Mark > > On 03/04/2015 10:03 am, "NISHA Prakash" wrote: > > > > > Hi, > > > > > > Can somebody please help with WHAM reweighting scheme for REMD > analysis. > > > The command "gmx wham" works for Umbrella sampling simulation but I > > couldnt > > > find a way out for T-REMD. > > > There are similar questions which have been posted here but > > unfortunately, > > > I haven't found answers for the same. > > > WHAM for REMD has been well documented for AMBER but I couldnt find any > > > help for Gromacs. > > > I am a novice in the field and help is appreciated. > > > > > > Thanks! > > > > > > Nisha > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
On 03/04/2015 5:53 pm, "Mark Abraham" wrote: > > Hi, > > I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation. i.e. The use of sed or similar tools is normal, as Tsjerk says also. There are too many options, and nobody has built the Babel fish of MD input! Mark > Mark > > On 03/04/2015 3:40 pm, "Alex" wrote: >> >> Mark, >> >> >> Not to troll, but why did you assume that I didn't do my due diligence before posting here? >> >> Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting. >> >> >> Alex >> >> >> >> > >> >> Hi, >> >> Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you. >> >> Mark >> >> On 03/04/2015 7:03 am, "Alex" wrote: >> >> >> I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it. >> >> I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is. >> >> >> ChemOffice produced a PDB with incompatible atom types. make-na server ( http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy. >> >> >> I will really appreciate any suggestions. >> >> >> Thank you, >> >> >> Alex >> >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> >> >> >> >> >> -- >> >> Best regards, >> >> Alexmailto:nedoma...@gmail.com >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Is_trjcat_suitable_for_concatenating_REMD_trajectorie
Hi Mark, All I want to know is the first step that I have to take in analyzing the trajectories. By way of mentioning what I want to do was to essentially list out my aim only to make my question clear. With REMD results, I want to know whether analyzing individual ensemble is the way to go or look at the ensembles together, this is because I would like to bring out a comparison between the simulations with protein bound to three different ligands. I hope I have made myself clear. Thanks again, Nisha On Fri, Apr 3, 2015 at 9:33 PM, Mark Abraham wrote: > Hi, > > You seem to be essentially asking for your experiment to be designed for > you, after an arbitrary simulation is complete. You should think about what > and how to observe before you simulate, e.g. from what others have done for > similar systems. > > Consideration of reweighting is secondary. Generally, the only difference > with REMD simulations is that you cannot assume that the set of frames from > an ensemble are from a contiguous trajectory. > > Mark > On 03/04/2015 11:21 am, "NISHA Prakash" wrote: > > > Hi Mark, > > > > Thanks for your quick response. > > Can you please suggest a way out? > > As you pointed out previously, I have 18 ensembles and I would like to > > study the conformational changes, the interactions between the protein > and > > the ligand and finally, I would like to extract the stable conformation > > from the simulation data. > > How do I go about analysing the REMD results. > > Your tutorial was indeed very helpful but apart from that, I couldn't > find > > much information in that area. > > > > Thanks again, > > Nisha > > > > On Fri, Apr 3, 2015 at 2:38 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > There's nothing in GROMACS that specifically supports reweighting > > > replica-exchange simulations. > > > > > > Mark > > > On 03/04/2015 10:03 am, "NISHA Prakash" > wrote: > > > > > > > Hi, > > > > > > > > Can somebody please help with WHAM reweighting scheme for REMD > > analysis. > > > > The command "gmx wham" works for Umbrella sampling simulation but I > > > couldnt > > > > find a way out for T-REMD. > > > > There are similar questions which have been posted here but > > > unfortunately, > > > > I haven't found answers for the same. > > > > WHAM for REMD has been well documented for AMBER but I couldnt find > any > > > > help for Gromacs. > > > > I am a novice in the field and help is appreciated. > > > > > > > > Thanks! > > > > > > > > Nisha > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Alex, You can use X3DNA to produce any nucleic acid geometry you’d like and gromacs pdb2gmx will understand it. For example, to create a single-strand of 16 DNA bases you only need a file with the corresponding rigid-body base-step parameters such as the ssdna.par file shown below: 16 # bases 0 # ***local step parameters*** # Shift Slide Rise Tilt Roll Twist T 0.000 0.000 0.000 0.000 0.000 0.000 A 0.280-0.664 3.201 2.499-2.89532.486 C -0.314-0.644 2.640 8.643 2.63128.956 C 0.424-0.849 3.240 1.756 1.69033.400 A 1.519-0.396 3.077 4.184 6.15239.140 A 0.412-0.670 2.797 6.57711.30926.608 C -0.183-2.185 2.859 6.133 5.12617.125 A 0.423-1.477 6.195 -18.545 -26.69136.074 C 1.216-0.879 3.063 5.417 8.46635.858 A -9.111-4.794-5.43374.82943.216 -56.814 C 3.440 0.344 3.176 3.03612.62142.046 A -9.111-4.794-5.43374.82943.216 -56.814 C 3.440 0.344 3.176 3.03612.62142.046 A 1.478 0.681 3.05613.088 0.20844.226 A -0.358-0.777 3.494-2.803-4.53433.162 A -0.264-0.272 2.833 9.637 1.45730.508 With such a file at hand all you have to do is issue the following two commands to 3DNA. x3dna_utils cp_std -d BDNA Which copies a standard BDNA backbone scaffold in the folder you’re at, and then: rebuild -atomic ssdna.par ssdna.pdb This will generate the file ssdna.pdb which you can find at: http://wikisend.com/download/614970/ssdna.pdb It works with: pdb2gmx -f ssdna.pdb -o start.pdb -p topol.top -i posre.itp -ff charmm27 -water tip3p In principle the online version of 3DNA, w3dna, would also work for generating nucleic acid models of any desired sequence. But sadly the X3DNA version working in the backend of the webserver is awfully outdated and uses the old convention of simply A, G, T, C, instead of DA, DG, DT, DC, to name the nucleotide residues. Hope this helps, Mauricio +++ Mauricio Esguerra Neira, Ph.D. Post-Doctoral Fellow Hugo Gutiérrez de Terán P.I. Department of Cell and Molecular Biology Uppsala University Phone Number: (+46)073-678-5334 mesguerra.org mauricio.esgue...@icm.uu.se +++ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Gentlemen, Building a script to rename the atom is obviously an option. I was just wondering if I missed something, e.g. a VMD plugin that could do it quickly. As far as google searching, I have done that, and I have found some things (like the make-NA server, or this: http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite what I was aiming for. Hence, my initial question. I didn't mean to be snippy, but I did try searching, believe me. On the other hand, I assume that you are much better versed in the problem at hand, so then maybe you'd be able to appreciate info I simply ignored. Obviously, I welcome anything you can suggest. If this boils down to me writing a renaming script, so be it. :) Thanks, Alex > On 03/04/2015 5:53 pm, "Mark Abraham"wrote: > > Hi, > > I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation. i.e. The use of sed or similar tools is normal, as Tsjerk says also. There are too many options, and nobody has built the Babel fish of MD input! Mark > Mark > > On 03/04/2015 3:40 pm, "Alex" wrote: >> >> Mark, >> >> >> Not to troll, but why did you assume that I didn't do my due diligence before posting here? >> >> Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting. >> >> >> Alex >> >> >> >> > >> >> Hi, >> >> Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you. >> >> Mark >> >> On 03/04/2015 7:03 am, "Alex" wrote: >> >> >> I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it. >> >> I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is. >> >> >> ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy. >> >> >> I will really appreciate any suggestions. >> >> >> Thank you, >> >> >> Alex >> >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> >> >> >> >> >> -- >> >> Best regards, >> >> Alex mailto:nedoma...@gmail.com >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Mauricio, That is very useful, thanks a lot. I'll try it in a bit. Alex MEN> Alex, MEN> You can use X3DNA to produce any nucleic acid geometry you’d like and MEN> gromacs pdb2gmx will understand it. MEN> For example, to create a single-strand of 16 DNA bases you only need a file MEN> with the corresponding rigid-body base-step parameters such as the MEN> ssdna.par file shown below: MEN> 16 # bases MEN>0 # ***local step parameters*** MEN> # Shift Slide Rise Tilt Roll Twist MEN> T 0.000 0.000 0.000 0.000 0.000 0.000 MEN> A 0.280-0.664 3.201 2.499-2.89532.486 MEN> C -0.314-0.644 2.640 8.643 2.63128.956 MEN> C 0.424-0.849 3.240 1.756 1.69033.400 MEN> A 1.519-0.396 3.077 4.184 6.15239.140 MEN> A 0.412-0.670 2.797 6.57711.30926.608 MEN> C -0.183-2.185 2.859 6.133 5.12617.125 MEN> A 0.423-1.477 6.195 -18.545 -26.69136.074 MEN> C 1.216-0.879 3.063 5.417 8.46635.858 MEN> A -9.111-4.794-5.43374.82943.216 -56.814 MEN> C 3.440 0.344 3.176 3.03612.62142.046 MEN> A -9.111-4.794-5.43374.82943.216 -56.814 MEN> C 3.440 0.344 3.176 3.03612.62142.046 MEN> A 1.478 0.681 3.05613.088 0.20844.226 MEN> A -0.358-0.777 3.494-2.803-4.53433.162 MEN> A -0.264-0.272 2.833 9.637 1.45730.508 MEN> With such a file at hand all you have to do is issue the following two MEN> commands to 3DNA. MEN> x3dna_utils cp_std -d BDNA MEN> Which copies a standard BDNA backbone scaffold in the folder you’re at, and MEN> then: MEN> rebuild -atomic ssdna.par ssdna.pdb MEN> This will generate the file ssdna.pdb which you can find at: MEN> http://wikisend.com/download/614970/ssdna.pdb MEN> It works with: MEN> pdb2gmx -f ssdna.pdb -o start.pdb -p topol.top -i posre.itp -ff MEN> charmm27 -water tip3p MEN> In principle the online version of 3DNA, w3dna, would also work for MEN> generating nucleic acid models of any desired sequence. But sadly the X3DNA MEN> version working in the backend of the webserver is awfully outdated and MEN> uses the old convention of simply A, G, T, C, instead of DA, DG, DT, DC, to MEN> name the nucleotide residues. MEN> Hope this helps, MEN> Mauricio MEN> +++ MEN> Mauricio Esguerra Neira, Ph.D. MEN> Post-Doctoral Fellow MEN> Hugo Gutiérrez de Terán P.I. MEN> Department of Cell and Molecular Biology MEN> Uppsala University MEN> Phone Number: (+46)073-678-5334 MEN> mesguerra.org MEN> mauricio.esgue...@icm.uu.se MEN> +++ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Hi Alex, Writing a sed oneliner is not the same as writing a renaming script. I commonly use them to process PDB files in some way and it's surprising how much you can do without scripting. Cheers, Tsjerk On Apr 3, 2015 7:13 PM, "Alex" wrote: > Gentlemen, > > > Building a script to rename the atom is obviously an option. I was just > wondering if I missed something, e.g. a VMD plugin that could do it > quickly. As far as google searching, I have done that, and I have found > some things (like the make-NA server, or this: > http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite > what I was aiming for. Hence, my initial question. I didn't mean to be > snippy, but I did try searching, believe me. On the other hand, I assume > that you are much better versed in the problem at hand, so then maybe you'd > be able to appreciate info I simply ignored. Obviously, I welcome anything > you can suggest. If this boils down to me writing a renaming script, so be > it. :) > > > Thanks, > > > Alex > > > > > > > > On 03/04/2015 5:53 pm, "Mark Abraham" wrote: > > > > > > Hi, > > > > > > I tried that search myself and found some things that looked potentially > useful to you, so I suggested that search. Either you might find something > useful there, or the dialogue could progress about what you need. Requiring > perfect input for pdb2gmx is a fairly stringent expectation. > > i.e. The use of sed or similar tools is normal, as Tsjerk says also. There > are too many options, and nobody has built the Babel fish of MD input! > > Mark > > > Mark > > > > > > On 03/04/2015 3:40 pm, "Alex" wrote: > > >> > > >> Mark, > > >> > > >> > > >> Not to troll, but why did you assume that I didn't do my due diligence > before posting here? > > >> > > >> Because, you see, you could have left that second part of your reply > (which only confirms the legitimacy of my initial question), and it would > make it less insulting. > > >> > > >> > > >> Alex > > >> > > >> > > >> > > >> > > > >> > > >> Hi, > > >> > > >> Googling things like "gromacs DNA structure" is a good bet. There are > no fully standardised naming schemes or workflows, so you will likely not > have something do everything for you. > > >> > > >> Mark > > >> > > >> On 03/04/2015 7:03 am, "Alex" wrote: > > >> > > >> > > >> I'm fully aware that this is a forum for discussing Gromacs, but > there's a bit of a frustrating situation that involves using it. > > >> > > >> I need a linear ssDNA chain, sequence of my choosing, anything that > will work with, say, AMBER99SB-ILDN. Not trying to find any funny > forcefields for it, everything as is. You suggested AMBER in the past, so > AMBER it is. > > >> > > >> > > >> ChemOffice produced a PDB with incompatible atom types. make-na server ( > http://structure.usc.edu/make-na/server.html) also produced something > pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a > usable topology out of the box with an established potential implemented in > Gromacs? Anything that will not involve manual modification of PDBs or > writing text-processing scripts will make me very happy. > > >> > > >> > > >> I will really appreciate any suggestions. > > >> > > >> > > >> Thank you, > > >> > > >> > > >> Alex > > >> > > >> > > >> > > >> > > >> -- > > >> > > >> Gromacs Users mailing list > > >> > > >> > > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > >> > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> > > >> * For (un)subscribe requests visit > > >> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > >> > > >> > > >> > > >> > > >> > > >> -- > > >> > > >> Best regards, > > >> > > >> Alexmailto:nedoma...@gmail.com > > >> > > >> > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> * For (un)subscribe requests visit > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > Best regards, > > Alexmailto:nedoma...@gmail.com > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mail
Re: [gmx-users] GMX-compatible DNA coordinates
Hi Tsjerk, You're right. It's just that the last time I used a sed or awk script of my own composition was in college, which is ~13 years ago. :)) So, this is still an undertaking for someone like me. But yes, what you said is well taken. Lack of knowledge/desire to rename atoms in text files shouldn't hinder research. I do think that having a person such as yourself of Justin on my team to implement what I have in mind would speed things up tremendously, but noone seems to be interested, hint-hint. ;) Thanks, Alex > Hi Alex, Writing a sed oneliner is not the same as writing a renaming script. I commonly use them to process PDB files in some way and it's surprising how much you can do without scripting. Cheers, Tsjerk On Apr 3, 2015 7:13 PM, "Alex"wrote: Gentlemen, Building a script to rename the atom is obviously an option. I was just wondering if I missed something, e.g. a VMD plugin that could do it quickly. As far as google searching, I have done that, and I have found some things (like the make-NA server, or this: http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite what I was aiming for. Hence, my initial question. I didn't mean to be snippy, but I did try searching, believe me. On the other hand, I assume that you are much better versed in the problem at hand, so then maybe you'd be able to appreciate info I simply ignored. Obviously, I welcome anything you can suggest. If this boils down to me writing a renaming script, so be it. :) Thanks, Alex > On 03/04/2015 5:53 pm, "Mark Abraham" wrote: > > Hi, > > I tried that search myself and found some things that looked potentially useful to you, so I suggested that search. Either you might find something useful there, or the dialogue could progress about what you need. Requiring perfect input for pdb2gmx is a fairly stringent expectation. i.e. The use of sed or similar tools is normal, as Tsjerk says also. There are too many options, and nobody has built the Babel fish of MD input! Mark > Mark > > On 03/04/2015 3:40 pm, "Alex" wrote: >> >> Mark, >> >> >> Not to troll, but why did you assume that I didn't do my due diligence before posting here? >> >> Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting. >> >> >> Alex >> >> >> >> > >> >> Hi, >> >> Googling things like "gromacs DNA structure" is a good bet. There are no fully standardised naming schemes or workflows, so you will likely not have something do everything for you. >> >> Mark >> >> On 03/04/2015 7:03 am, "Alex" wrote: >> >> >> I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it. >> >> I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is. >> >> >> ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy. >> >> >> I will really appreciate any suggestions. >> >> >> Thank you, >> >> >> Alex >> >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> >> >> >> >> >> -- >> >> Best regards, >> >> Alex mailto:nedoma...@gmail.com >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Best regards, Alex
[gmx-users] the study of concentration effect in gromacs
Dear All i know for increasing ions in gromacs, we have to using GENION tool but i dont know how increase or change * the protein* or drug concentration in gromacs. i ll really apriciate for any response -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Hi Alex, I've done it before, but I can't do it from the top of my head without seeing the input and checking what Gromacs wants. It's not hard work, it's not a lot of work, but it is work, and more than we'll usually consider doing for answering a post on the mailing list. On the other hand, you can always try to raise interest in a collaboration, which is a completely different matter :) Cheers, Tsjerk On Fri, Apr 3, 2015 at 8:21 PM, Alex wrote: > Hi Tsjerk, > > > You're right. It's just that the last time I used a sed or awk script of > my own composition was in college, which is ~13 years ago. :)) > > So, this is still an undertaking for someone like me. But yes, what you > said is well taken. Lack of knowledge/desire to rename atoms in text files > shouldn't hinder research. > > I do think that having a person such as yourself of Justin on my team to > implement what I have in mind would speed things up tremendously, but noone > seems to be interested, hint-hint. ;) > > > Thanks, > > > Alex > > > > > > > Hi Alex, > > Writing a sed oneliner is not the same as writing a renaming script. I > commonly use them to process PDB files in some way and it's surprising how > much you can do without scripting. > > Cheers, > > Tsjerk > > On Apr 3, 2015 7:13 PM, "Alex" wrote: > > > Gentlemen, > > > Building a script to rename the atom is obviously an option. I was just > wondering if I missed something, e.g. a VMD plugin that could do it > quickly. As far as google searching, I have done that, and I have found > some things (like the make-NA server, or this: > http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite > what I was aiming for. Hence, my initial question. I didn't mean to be > snippy, but I did try searching, believe me. On the other hand, I assume > that you are much better versed in the problem at hand, so then maybe you'd > be able to appreciate info I simply ignored. Obviously, I welcome anything > you can suggest. If this boils down to me writing a renaming script, so be > it. :) > > > Thanks, > > > Alex > > > > > > > > On 03/04/2015 5:53 pm, "Mark Abraham" wrote: > > > > > > Hi, > > > > > > I tried that search myself and found some things that looked potentially > useful to you, so I suggested that search. Either you might find something > useful there, or the dialogue could progress about what you need. Requiring > perfect input for pdb2gmx is a fairly stringent expectation. > > i.e. The use of sed or similar tools is normal, as Tsjerk says also. There > are too many options, and nobody has built the Babel fish of MD input! > > Mark > > > Mark > > > > > > On 03/04/2015 3:40 pm, "Alex" wrote: > > >> > > >> Mark, > > >> > > >> > > >> Not to troll, but why did you assume that I didn't do my due diligence > before posting here? > > >> > > >> Because, you see, you could have left that second part of your reply > (which only confirms the legitimacy of my initial question), and it would > make it less insulting. > > >> > > >> > > >> Alex > > >> > > >> > > >> > > >> > > > >> > > >> Hi, > > >> > > >> Googling things like "gromacs DNA structure" is a good bet. There are > no fully standardised naming schemes or workflows, so you will likely not > have something do everything for you. > > >> > > >> Mark > > >> > > >> On 03/04/2015 7:03 am, "Alex" wrote: > > >> > > >> > > >> I'm fully aware that this is a forum for discussing Gromacs, but > there's a bit of a frustrating situation that involves using it. > > >> > > >> I need a linear ssDNA chain, sequence of my choosing, anything that > will work with, say, AMBER99SB-ILDN. Not trying to find any funny > forcefields for it, everything as is. You suggested AMBER in the past, so > AMBER it is. > > >> > > >> > > >> ChemOffice produced a PDB with incompatible atom types. make-na server ( > http://structure.usc.edu/make-na/server.html) also produced something > pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a > usable topology out of the box with an established potential implemented in > Gromacs? Anything that will not involve manual modification of PDBs or > writing text-processing scripts will make me very happy. > > >> > > >> > > >> I will really appreciate any suggestions. > > >> > > >> > > >> Thank you, > > >> > > >> > > >> Alex > > >> > > >> > > >> > > >> > > >> -- > > >> > > >> Gromacs Users mailing list > > >> > > >> > > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > >> > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> > > >> * For (un)subscribe requests visit > > >> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > >> > > >> > > >> > > >> > > >> > > >> -- > > >> > > >> Best regards, > > >> > > >> Alexmailto:nedoma...@gmail.com > > >> > > >> > > >> -- > > >> Gromacs Users mailing lis
Re: [gmx-users] the study of concentration effect in gromacs
Hi Elham, You can increase the protein concentration by using a smaller box, or by putting two or more proteins in a box together. With drugs, you can raise the concentration by adding more, using the insert option of genbox. Cheers, Tsjerk On Fri, Apr 3, 2015 at 9:13 PM, elham tazikeh wrote: > Dear All > i know for increasing ions in gromacs, we have to using GENION tool > but i dont know how increase or change * the protein* or drug concentration > in gromacs. > i ll really apriciate for any response > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX-compatible DNA coordinates
Tsjerk, I can only describe the project in a private communication, as this is a completely new idea (potentially high-risk from the experimental standpoint) in a very competitive field. If you're interested, please let me know, and I'll email you directly. Other than that, there is not much I can reveal on a public forum. I hope you'll understand. ;) Alex On Fri, Apr 3, 2015 at 1:33 PM, Tsjerk Wassenaar wrote: > Hi Alex, > > I've done it before, but I can't do it from the top of my head without > seeing the input and checking what Gromacs wants. It's not hard work, it's > not a lot of work, but it is work, and more than we'll usually consider > doing for answering a post on the mailing list. On the other hand, you can > always try to raise interest in a collaboration, which is a completely > different matter :) > > Cheers, > > Tsjerk > > > On Fri, Apr 3, 2015 at 8:21 PM, Alex wrote: > >> Hi Tsjerk, >> >> >> You're right. It's just that the last time I used a sed or awk script of >> my own composition was in college, which is ~13 years ago. :)) >> >> So, this is still an undertaking for someone like me. But yes, what you >> said is well taken. Lack of knowledge/desire to rename atoms in text files >> shouldn't hinder research. >> >> I do think that having a person such as yourself of Justin on my team to >> implement what I have in mind would speed things up tremendously, but noone >> seems to be interested, hint-hint. ;) >> >> >> Thanks, >> >> >> Alex >> >> >> >> > >> >> Hi Alex, >> >> Writing a sed oneliner is not the same as writing a renaming script. I >> commonly use them to process PDB files in some way and it's surprising how >> much you can do without scripting. >> >> Cheers, >> >> Tsjerk >> >> On Apr 3, 2015 7:13 PM, "Alex" wrote: >> >> >> Gentlemen, >> >> >> Building a script to rename the atom is obviously an option. I was just >> wondering if I missed something, e.g. a VMD plugin that could do it >> quickly. As far as google searching, I have done that, and I have found >> some things (like the make-NA server, or this: >> http://smog-server.org/cgi-bin/GenTopGro.pl). This is still not quite >> what I was aiming for. Hence, my initial question. I didn't mean to be >> snippy, but I did try searching, believe me. On the other hand, I assume >> that you are much better versed in the problem at hand, so then maybe you'd >> be able to appreciate info I simply ignored. Obviously, I welcome anything >> you can suggest. If this boils down to me writing a renaming script, so be >> it. :) >> >> >> Thanks, >> >> >> Alex >> >> >> >> > >> >> >> On 03/04/2015 5:53 pm, "Mark Abraham" wrote: >> >> > >> >> > Hi, >> >> > >> >> > I tried that search myself and found some things that looked >> potentially useful to you, so I suggested that search. Either you might >> find something useful there, or the dialogue could progress about what you >> need. Requiring perfect input for pdb2gmx is a fairly stringent expectation. >> >> i.e. The use of sed or similar tools is normal, as Tsjerk says also. >> There are too many options, and nobody has built the Babel fish of MD >> input! >> >> Mark >> >> > Mark >> >> > >> >> > On 03/04/2015 3:40 pm, "Alex" wrote: >> >> >> >> >> >> Mark, >> >> >> >> >> >> >> >> >> Not to troll, but why did you assume that I didn't do my due diligence >> before posting here? >> >> >> >> >> >> Because, you see, you could have left that second part of your reply >> (which only confirms the legitimacy of my initial question), and it would >> make it less insulting. >> >> >> >> >> >> >> >> >> Alex >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> Hi, >> >> >> >> >> >> Googling things like "gromacs DNA structure" is a good bet. There are >> no fully standardised naming schemes or workflows, so you will likely not >> have something do everything for you. >> >> >> >> >> >> Mark >> >> >> >> >> >> On 03/04/2015 7:03 am, "Alex" wrote: >> >> >> >> >> >> >> >> >> I'm fully aware that this is a forum for discussing Gromacs, but >> there's a bit of a frustrating situation that involves using it. >> >> >> >> >> >> I need a linear ssDNA chain, sequence of my choosing, anything that >> will work with, say, AMBER99SB-ILDN. Not trying to find any funny >> forcefields for it, everything as is. You suggested AMBER in the past, so >> AMBER it is. >> >> >> >> >> >> >> >> >> ChemOffice produced a PDB with incompatible atom types. make-na server >> (http://structure.usc.edu/make-na/server.html) also produced something >> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a >> usable topology out of the box with an established potential implemented in >> Gromacs? Anything that will not involve manual modification of PDBs or >> writing text-processing scripts will make me very happy. >> >> >> >> >> >> >> >> >> I will really appreciate any suggestions. >> >> >> >> >> >> >> >> >> Thank you, >> >> >> >> >> >> >> >> >> Alex >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >>
[gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?
Dear gromacs users Hello. I have question how to decide terminal residue forcefield and put them in library? I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls forcefield, amber forcefield treat termini in its own way and current version only works with NH3+ and COO-. I would like to termini as a neutral status, NH2 and COOH and would like to modify forcefield to include this specific termini data. To decide charges and parameters to describe specific termini, is there any way to decide parameters based on non-terminal residue database? When I looked at NGLY and GLY from animoacids.rtp, I could not find out specific rules. Thank you very much. Sangeun Jee -- Post Doctoral Researcher School of Materials Science and Engineering Georgia Institute of Technology -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?
Dear Sangeun, Did you try ‘pdb2gmx’ using your structure file? I checked NME and NHE are in the AMBER99sb-ildn forecefield. So, if pdb2gmx doesn’t work, you can draw NME and NHE using molecular viewer and then change residue/atom name to NME and NHE. Yoochan > On Apr 4, 2015, at 7:01 AM, sang eun jee wrote: > > Dear gromacs users > > Hello. I have question how to decide terminal residue forcefield and put > them in library? > > I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls > forcefield, amber forcefield treat termini in its own way and current > version only works with NH3+ and COO-. I would like to termini as a neutral > status, NH2 and COOH and would like to modify forcefield to include this > specific termini data. > > To decide charges and parameters to describe specific termini, is there any > way to decide parameters based on non-terminal residue database? When I > looked at NGLY and GLY from animoacids.rtp, I could not find out specific > rules. > > Thank you very much. > > Sangeun Jee > -- > Post Doctoral Researcher > School of Materials Science and Engineering > Georgia Institute of Technology > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.