Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
Hi, Adding a bit to Mark here... > I am reasonably certain that if I put in more than > > one copy of something which is in a .rtp file and _not_ in, say, > ions.itp, > > then it will be in both times in the .top file > > I think you are missing a point or two in comprehension here. The .rtp > file is a database used only by pdb2gmx to help construct a > correctly-connected topology for the residues in that database. I don't > know about the behaviour of pdb2gmx on a structure file with multiple > copies of the same molecule in different chains, but if it works, I > expect it won't notice the same molecule is the product, and would thus > produce two differently-named [ molecule ] sections for a dimeric > system. In any case, the OP did not need to have been using pdb2gmx, and > so the contents of the .rtp file are a red herring. This is of course very common with multimeric proteins, and Mark is right: pdb2gmx converts each chain it encounters to a "moleculetype". This has nothing to do with whatever is in the .rtp database. > (after all, two > > different-position glycines are in twice in the .top file...). > > pdb2gmx has atoms and residues as its two levels of structure. ...and a third level: chains (which are translated to moleculetypes and are a rough approximation of molecules). The topology file has atoms and molecules as its two levels of structure. In > the latter, residue names and numbers are retained purely for human > convenience, say, in constructing index groups. Since these glycine > residues are parts of molecules, they have to be replicated. This has > nothing to do with replication of molecules, however. You could define > multiple different [ molecule ] sections with different names for the > same molecule and then have multiple entries in the [ molecules ] > section, or you could have just one and have a single entry in the [ > molecules ] section. This brings us back to my original point that in > the latter case the numbering of the atoms in [ molecule ] sections does > not need to correspond to the structure file. > > Someone should definitely (re)read Chapter 5 of the manual... (and it's not Mark ;)). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
Allen Smith wrote: which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which I obtained from the original top file by simply changing the number of residues of each group in the last section. Umm... the atom numbers (not just the numbers of residues) are going to need to correspond between the .top and .gro files. I think the OP meant changing the number of molecules in the [molecules] section of the .top file. I expect that within each molecule in the structure file the order of the atoms must agree between with the topology file. Certainly the order of the molecules in the [molecules] section must correspond to that in the structure file. However, the atom numbers cannot (in general), match in order between structure and topology file for any system with more than one copy of a molecule (e.g. solvent). For simple solvated systems where one gets focussed on the solute, it can look like correspondence is occurring and thus might be necessary :-) However, in this case, the original poster has not only edited down the solvent, but the bilayer. The bilayer is just another set of molecules, like the solvent. There's nothing magical. As above, assuming the OP mis-used "residues" for "molecules" then they're on the right track for this part of the problem. I am reasonably certain that if I put in more than one copy of something which is in a .rtp file and _not_ in, say, ions.itp, then it will be in both times in the .top file I think you are missing a point or two in comprehension here. The .rtp file is a database used only by pdb2gmx to help construct a correctly-connected topology for the residues in that database. I don't know about the behaviour of pdb2gmx on a structure file with multiple copies of the same molecule in different chains, but if it works, I expect it won't notice the same molecule is the product, and would thus produce two differently-named [ molecule ] sections for a dimeric system. In any case, the OP did not need to have been using pdb2gmx, and so the contents of the .rtp file are a red herring. (after all, two different-position glycines are in twice in the .top file...). pdb2gmx has atoms and residues as its two levels of structure. The topology file has atoms and molecules as its two levels of structure. In the latter, residue names and numbers are retained purely for human convenience, say, in constructing index groups. Since these glycine residues are parts of molecules, they have to be replicated. This has nothing to do with replication of molecules, however. You could define multiple different [ molecule ] sections with different names for the same molecule and then have multiple entries in the [ molecules ] section, or you could have just one and have a single entry in the [ molecules ] section. This brings us back to my original point that in the latter case the numbering of the atoms in [ molecule ] sections does not need to correspond to the structure file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
Hi, I've noticed this too and indeed it can be a bit irritating. For example: editconf doesn't recognize the HOH residue when changing the box density (see also http://www.gromacs.org/pipermail/gmx-users/2007-January/025611.html). Of course it's not a big problem, and maybe there's a very good reason why pdb2gmx is doing this. Then again, if not, maybe it can be changed. Thanks, Jeroen >Date: Wed, 3 Oct 2007 19:09:54 -0400 >From: Allen Smith <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] getting a good .gro file from a pdb file > while the topology is ready >To: gmx-users@gromacs.org >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >[...] > >P.S. Incidentally, I note the irritating habit of pdb2gmx (including in >3.3.2) of converting what is already labeled as SOL to HOH, >even though genbox inserts water molecules as SOL. > >-- >Allen Smith ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
In message <[EMAIL PROTECTED]> (on 3 October 2007 19:09:54 -0400), [EMAIL PROTECTED] (Allen Smith) wrote: >In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000), >[EMAIL PROTECTED] (Mark Abraham) wrote: >>Allen Smith wrote: >>> Umm... the atom numbers (not just the numbers of residues) are going to >>> need to correspond between the .top and .gro files. >> >>I think the OP meant changing the number of molecules in the [molecules] >>section of the .top file. I expect that within each molecule in the >>structure file the order of the atoms must agree between with the >>topology file. Certainly the order of the molecules in the [molecules] >>section must correspond to that in the structure file. >> >>However, the atom numbers cannot (in general), match in order between >>structure and topology file for any system with more than one copy of a >>molecule (e.g. solvent). For simple solvated systems where one gets >>focussed on the solute, it can look like correspondence is occurring and >>thus might be necessary :-) > >However, in this case, the original poster has not only edited down the >solvent, but the bilayer. I am reasonably certain that if I put in more than >one copy of something which is in a .rtp file and _not_ in, say, ions.itp, >then it will be in both times in the .top file (after all, two >different-position glycines are in twice in the .top file...). Correction: multiple copies of an ion present in the .pdb file input into pdb2gmx come out multiple times in the .top file (even though the ion is in ions.itp), at least for a case in which they're not distinguished by chain id from the rest. -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ September 11, 2001 A Day That Shall Live In Infamy II "They that can give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." - Benjamin Franklin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000), [EMAIL PROTECTED] (Mark Abraham) wrote: >Allen Smith wrote: >> In message <[EMAIL PROTECTED]> (on >> 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) >> wrote: >>> Hi, >>> >>> I had a large bilayer in .gro and .top gromacs format files >> >> Bilayer? I believe there are some specific things for doing planar periodic >> boundary conditions (or planar infinite system conditions), but I am not >> familiar with them. > >Yeah but they're in the .mdp and not the issue here :-) Ah, thank you. > >>> which I truncated to make a smaller bilayer, and added some more water >>> molecules, using programs other than gromacs. The final output I have is a >>> pdb file with complete solvation, and a topology file which I obtained from >>> the original top file by simply changing the number of residues of each >>> group in the last section. >> >> Umm... the atom numbers (not just the numbers of residues) are going to need >> to correspond between the .top and .gro files. > >I think the OP meant changing the number of molecules in the [molecules] >section of the .top file. I expect that within each molecule in the >structure file the order of the atoms must agree between with the >topology file. Certainly the order of the molecules in the [molecules] >section must correspond to that in the structure file. > >However, the atom numbers cannot (in general), match in order between >structure and topology file for any system with more than one copy of a >molecule (e.g. solvent). For simple solvated systems where one gets >focussed on the solute, it can look like correspondence is occurring and >thus might be necessary :-) However, in this case, the original poster has not only edited down the solvent, but the bilayer. I am reasonably certain that if I put in more than one copy of something which is in a .rtp file and _not_ in, say, ions.itp, then it will be in both times in the .top file (after all, two different-position glycines are in twice in the .top file...). There may be some dependence on chain labels from the original .pdb file, however, from observations; I suppose that it's possible that it would partially depend on whether the name is in aminoacid.dat or something like that, although that seems a bit weird. It doesn't sound like the original poster is using something that's in an .itp file that the original poster has constructed. -Allen P.S. Incidentally, I note the irritating habit of pdb2gmx (including in 3.3.2) of converting what is already labeled as SOL to HOH, even though genbox inserts water molecules as SOL. -- Allen Smith http://cesario.rutgers.edu/easmith/ There is only one sound argument for democracy, and that is the argument that it is a crime for any man to hold himself out as better than other men, and, above all, a most heinous offense for him to prove it. - H. L. Mencken ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
On Wed, 3 Oct 2007 19:13:51 +0200 "maria goranovic" <[EMAIL PROTECTED]> wrote: Hi, I had a large bilayer in .gro and .top gromacs format files which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which I obtained from the original top file by simply changing the number of residues of each group in the last section. My goal is now to obtain a proper input to the grompp program, which is a good .gro and a .top file. The latter I already have. pdb2gmx is not working for me with the error: %Fatal error: %Residue 'DPP' not found in residue topology database This is because the pdb file truncates the name of your DPPC (I guess) molecules. just edit the pdb file you have and change the "DPP " to "DPPC". in vi you can do this by typing: :1,$ s/DPP /DPPC/ then editconf would allwo you to get a gro file but the pdb should be ok. Q1. How do I add my topology file to the database ? you have it already. Q2. The second question is regarding the use of genbox and editconf. How can I specify the box size such that no more solvent is added to the system ? just add the box size at the end of the gro file. Using the following two options adds more solvent to the system, which I do not really need % editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90 -bt triclinic -o input.gro -c -center 0 0 0 % genbox -cp input.gro -o output.gro -cs spc216.gro no need. I chose the box size based on the maximum and minimum coordinates of the heavy atoms of the system. Does one have to do the above procedure by iteratively changing the box size until genbox adds no more solvent ? just add the box size at the end of the gro file: boxX boxX boxZ Please do not be ruthless, I am new to gromacs :) Thank you, -- Maria G. Technical University of Denmark Copenhagen - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
Allen Smith wrote: In message <[EMAIL PROTECTED]> (on 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) wrote: Hi, I had a large bilayer in .gro and .top gromacs format files Bilayer? I believe there are some specific things for doing planar periodic boundary conditions (or planar infinite system conditions), but I am not familiar with them. Yeah but they're in the .mdp and not the issue here :-) which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which I obtained from the original top file by simply changing the number of residues of each group in the last section. Umm... the atom numbers (not just the numbers of residues) are going to need to correspond between the .top and .gro files. I think the OP meant changing the number of molecules in the [molecules] section of the .top file. I expect that within each molecule in the structure file the order of the atoms must agree between with the topology file. Certainly the order of the molecules in the [molecules] section must correspond to that in the structure file. However, the atom numbers cannot (in general), match in order between structure and topology file for any system with more than one copy of a molecule (e.g. solvent). For simple solvated systems where one gets focussed on the solute, it can look like correspondence is occurring and thus might be necessary :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
maria goranovic wrote: Hi, I had a large bilayer in .gro and .top gromacs format files which I truncated to make a smaller bilayer, and added some more water molecules, using programs other than gromacs. The final output I have is a pdb file with complete solvation, and a topology file which I obtained from the original top file by simply changing the number of residues of each group in the last section. My goal is now to obtain a proper input to the grompp program, which is a good .gro and a .top file. The latter I already have. pdb2gmx is not working for me with the error: The purpose of pdb2gmx is to infer topologies from structures. Since you have a working topology you don't need this step. %Fatal error: %Residue 'DPP' not found in residue topology database Q1. How do I add my topology file to the database ? Well, as above, you don't need it. Otherwise, you need to read chapter 5 of the manual and figure out how it is done. Q2. The second question is regarding the use of genbox and editconf. How can I specify the box size such that no more solvent is added to the system ? I don't understand your objective. If you don't want to add more solvent, don't use genbox. Using the following two options adds more solvent to the system, which I do not really need % editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90 -bt triclinic -o input.gro -c -center 0 0 0 % genbox -cp input.gro -o output.gro -cs spc216.gro I chose the box size based on the maximum and minimum coordinates of the heavy atoms of the system. Hydrogen takes up volume too... your equilibration will be less troublesome if your whole system "fits" at the start of the equilibration. It sounds like it might be worth your while reading the introductory part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea what each tool is trying to do. Following a recipe without appreciating what you're doing is fine, until you go to change the recipe, which is what you're trying to do here. :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
In message <[EMAIL PROTECTED]> (on 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic) wrote: >Hi, > >I had a large bilayer in .gro and .top gromacs format files Bilayer? I believe there are some specific things for doing planar periodic boundary conditions (or planar infinite system conditions), but I am not familiar with them. >which I truncated to make a smaller bilayer, and added some more water >molecules, using programs other than gromacs. The final output I have is a >pdb file with complete solvation, and a topology file which I obtained from >the original top file by simply changing the number of residues of each >group in the last section. Umm... the atom numbers (not just the numbers of residues) are going to need to correspond between the .top and .gro files. >My goal is now to obtain a proper input to the >grompp program, which is a good .gro and a .top file. The latter I already >have. > >pdb2gmx is not working for me with the error: > >%Fatal error: >%Residue 'DPP' not found in residue topology database > >Q1. How do I add my topology file to the database ? What is DPP? Perhaps it's under another name in the original .top and .gro files, in which case you should change the name in the .pdb file input to that name? >Q2. The second question is regarding the use of genbox and editconf. How can >I specify the box size such that no more solvent is added to the system ? > >Using the following two options adds more solvent to the system, which I do >not really need > >% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90 >-bt triclinic -o input.gro -c -center 0 0 0 I tend to use -princ, to align the longest axis of the input with the longest axis of the box (17.3 in your case). Not sure if that would be advisable with a bilayer system, however. >% genbox -cp input.gro -o output.gro -cs spc216.gro > >I chose the box size based on the maximum and minimum coordinates of the >heavy atoms of the system. Do heavy atoms include the oxygens in the waters? If so, then I would think that that should be an adequate size (I trust you allowed for gromacs using nanometers while PDB files use angstroms?); I would suspect things would be too crowded otherwise. However, if you use -princ, you will probably need to check to see exactly what dimensions it comes out to have prior to putting it into the box, since it may align it differently than it is already aligned. >Does one have to do the above procedure by >iteratively changing the box size until genbox adds no more solvent ? If you don't want more solvent added, don't use genbox. The question will be how to do this while making sure you don't have any vacuum spaces. -Allen -- Allen Smith http://cesario.rutgers.edu/easmith/ There is only one sound argument for democracy, and that is the argument that it is a crime for any man to hold himself out as better than other men, and, above all, a most heinous offense for him to prove it. - H. L. Mencken ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
