Re: [gmx-users] water clusters MD
In addition to Marks e-mail and in order to close the topic I suggest you to exempt people from your "mentor" comments in future. O. --- On Wed, 6/2/10, Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] water clusters MD > To: "Discussion list for GROMACS users" > Date: Wednesday, June 2, 2010, 9:52 AM > - Original Message - > From: Oleksandr > Date: Wednesday, June 2, 2010 13:12 > Subject: Re: [gmx-users] water clusters MD > To: Mark Abraham > > > There is some inconsistency between the top/itp > files that > > you provided. > > The grompp gives an error "Found a second defaults > directive." > > Please do not take discussions off the list. See > http://www.gromacs.org/Support for why. > > My suggested files are not inconsistent. I have only one > such directive and there's no way to get a second one > without you doing something wrong. I can't have any idea > what's happened since, and you haven't bothered to tell me. > This particular error occurs regularly with new users, and > is discussed here http://www.gromacs.org/Documentation/Errors. > > This goes to prove my point that you need more general > experience of GROMACS before tackling this specific problem. > Learn to walk before assuming you can run! > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water clusters MD
- Original Message - From: Oleksandr Date: Wednesday, June 2, 2010 13:12 Subject: Re: [gmx-users] water clusters MD To: Mark Abraham > There is some inconsistency between the top/itp files that > you provided. > The grompp gives an error "Found a second defaults directive." Please do not take discussions off the list. See http://www.gromacs.org/Support for why. My suggested files are not inconsistent. I have only one such directive and there's no way to get a second one without you doing something wrong. I can't have any idea what's happened since, and you haven't bothered to tell me. This particular error occurs regularly with new users, and is discussed here http://www.gromacs.org/Documentation/Errors. This goes to prove my point that you need more general experience of GROMACS before tackling this specific problem. Learn to walk before assuming you can run! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water clusters MD
- Original Message - From: Oleksandr Date: Tuesday, June 1, 2010 12:43 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users > It would be helpful if you could be more specific. For example, > the standard procedure described in tutorial: > > pdb2gmx -f input.pdb > edit conf -f conf.gro d 0.5 -o newbox.gro > genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb > > Now, could you please illustrate how would you do this for > "trivial" non-protein molecules? editconf -d 0.5 -f pentamer.pdb -o newbox.gro genbox -cp newbox.gro -cs -o solvated.gro You can get some more information with editconf -h and genbox -h. Mark > --- On Tue, 6/1/10, Mark Abraham wrote: > > > From: Mark Abraham > > Subject: Re: [gmx-users] water clusters MD > > To: "Discussion list for GROMACS users" > > Date: Tuesday, June 1, 2010, 4:16 AM > > - Original Message ----- > > From: Oleksandr > > Date: Tuesday, June 1, 2010 11:39 > > Subject: Re: [gmx-users] water clusters MD > > To: Discussion list for GROMACS users > > > > > Look, in order to use editconf and gen box one need > > first to > > > have gro and top files, which are generated by > > pdb2gmx. You say > > > > You need neither file for editconf and genbox. See > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file.> > You can use your existing correctly-formatted .pdb file. > > > > If you already have a .top for the original structure, > > genbox will update it suitably with the new waters. > > > > Mark > > > > > I don't need it. Ok may be topology file can be > > written by hand, > > > but what about "gro" file? > > > > > > --- On Mon, 5/31/10, Mark Abraham > > wrote: > > > > > > > From: Mark Abraham > > > > Subject: Re: [gmx-users] water clusters MD > > > > To: "Discussion list for GROMACS users" us...@gromacs.org>> > > Date: Monday, May 31, 2010, 10:55 AM > > > > - Original Message - > > > > From: Oleksandr > > > > Date: Monday, May 31, 2010 18:48 > > > > Subject: [gmx-users] water clusters MD > > > > To: gmx-users@gromacs.org > > > > > > > > > Hi, > > > > > I'm new user of Gromacs. There are plenty > > examples how > > > > to do > > > > > solvation study of various proteins. But I'd > > like to > > > > "solvate" > > > > > highly ordered heavy water clusters in box > > of light > > > > water. At > > > > > the first step when I execute "pdb2gmx -f > > > > watercluster.pdb" I > > > > > get an error no matter which model is > > chosen: > > > > > > > > > > > --- > > > > > > > > > > Fatal error: > > > > > Atom H in residue HOH 4 not found in rtp > > entry with 3 > > > > atoms > > > > > while sorting atoms. > > Maybe > > > > different protonation state. > > > > > Remove this hydrogen or > > choose a > > > > different > > > > > protonation state. > > > > > Option -ignh will > > ignore all > > > > hydrogens in the input. > > > > > > > > > > > --- > > > > > > > > > > Can anybody help me how to solve this > > problem? > > > > > > > > You're using a tool for a different job. pdb2gmx > > builds a > > > > topology file, mostly by constructing a > > [moleculetype] from > > > > a polymer of repeating units. Your moleculetypes > > are > > > > trivial, and at least one is already present in > > an .itp file > > > > for use with #include. > > > > > > > > editconf and genbox make a box and fill it with > > generic > > > > solvent. It will be simplest to either write your > > .top by > > > > hand, or adapt an existing .top, depending what > > you mean by > > > > "heavy water". Either way, you'll need some > > fluency with > > > > GROMACS workflows and file types, so do all the > > general > > > > tutorial material you can find.
Re: [gmx-users] water clusters MD
It would be helpful if you could be more specific. For example, the standard procedure described in tutorial: pdb2gmx -f input.pdb edit conf -f conf.gro d 0.5 -o newbox.gro genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb Now, could you please illustrate how would you do this for "trivial" non-protein molecules? --- On Tue, 6/1/10, Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] water clusters MD > To: "Discussion list for GROMACS users" > Date: Tuesday, June 1, 2010, 4:16 AM > - Original Message - > From: Oleksandr > Date: Tuesday, June 1, 2010 11:39 > Subject: Re: [gmx-users] water clusters MD > To: Discussion list for GROMACS users > > > Look, in order to use editconf and gen box one need > first to > > have gro and top files, which are generated by > pdb2gmx. You say > > You need neither file for editconf and genbox. See > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. > You can use your existing correctly-formatted .pdb file. > > If you already have a .top for the original structure, > genbox will update it suitably with the new waters. > > Mark > > > I don't need it. Ok may be topology file can be > written by hand, > > but what about "gro" file? > > > > --- On Mon, 5/31/10, Mark Abraham > wrote: > > > > > From: Mark Abraham > > > Subject: Re: [gmx-users] water clusters MD > > > To: "Discussion list for GROMACS users" > > > Date: Monday, May 31, 2010, 10:55 AM > > > - Original Message - > > > From: Oleksandr > > > Date: Monday, May 31, 2010 18:48 > > > Subject: [gmx-users] water clusters MD > > > To: gmx-users@gromacs.org > > > > > > > Hi, > > > > I'm new user of Gromacs. There are plenty > examples how > > > to do > > > > solvation study of various proteins. But I'd > like to > > > "solvate" > > > > highly ordered heavy water clusters in box > of light > > > water. At > > > > the first step when I execute "pdb2gmx -f > > > watercluster.pdb" I > > > > get an error no matter which model is > chosen: > > > > > > > > --- > > > > > > > > Fatal error: > > > > Atom H in residue HOH 4 not found in rtp > entry with 3 > > > atoms > > > > while sorting atoms. > Maybe > > > different protonation state. > > > > Remove this hydrogen or > choose a > > > different > > > > protonation state. > > > > Option -ignh will > ignore all > > > hydrogens in the input. > > > > > > > > --- > > > > > > > > Can anybody help me how to solve this > problem? > > > > > > You're using a tool for a different job. pdb2gmx > builds a > > > topology file, mostly by constructing a > [moleculetype] from > > > a polymer of repeating units. Your moleculetypes > are > > > trivial, and at least one is already present in > an .itp file > > > for use with #include. > > > > > > editconf and genbox make a box and fill it with > generic > > > solvent. It will be simplest to either write your > .top by > > > hand, or adapt an existing .top, depending what > you mean by > > > "heavy water". Either way, you'll need some > fluency with > > > GROMACS workflows and file types, so do all the > general > > > tutorial material you can find. If you'd done so, > you might > > > have realised that pdb2gmx is not really the tool > for the > > > job. > > > > > > Mark > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.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 gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Pleas
Re: [gmx-users] water clusters MD
- Original Message - From: Oleksandr Date: Tuesday, June 1, 2010 11:39 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users > Look, in order to use editconf and gen box one need first to > have gro and top files, which are generated by pdb2gmx. You say You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file. If you already have a .top for the original structure, genbox will update it suitably with the new waters. Mark > I don't need it. Ok may be topology file can be written by hand, > but what about "gro" file? > > --- On Mon, 5/31/10, Mark Abraham wrote: > > > From: Mark Abraham > > Subject: Re: [gmx-users] water clusters MD > > To: "Discussion list for GROMACS users" > > Date: Monday, May 31, 2010, 10:55 AM > > - Original Message ----- > > From: Oleksandr > > Date: Monday, May 31, 2010 18:48 > > Subject: [gmx-users] water clusters MD > > To: gmx-users@gromacs.org > > > > > Hi, > > > I'm new user of Gromacs. There are plenty examples how > > to do > > > solvation study of various proteins. But I'd like to > > "solvate" > > > highly ordered heavy water clusters in box of light > > water. At > > > the first step when I execute "pdb2gmx -f > > watercluster.pdb" I > > > get an error no matter which model is chosen: > > > > > --- > > > > > > Fatal error: > > > Atom H in residue HOH 4 not found in rtp entry with 3 > > atoms > > > while sorting atoms. Maybe > > different protonation state. > > > Remove this hydrogen or choose a > > different > > > protonation state. > > > Option -ignh will ignore all > > hydrogens in the input. > > > > > --- > > > > > > Can anybody help me how to solve this problem? > > > > You're using a tool for a different job. pdb2gmx builds a > > topology file, mostly by constructing a [moleculetype] from > > a polymer of repeating units. Your moleculetypes are > > trivial, and at least one is already present in an .itp file > > for use with #include. > > > > editconf and genbox make a box and fill it with generic > > solvent. It will be simplest to either write your .top by > > hand, or adapt an existing .top, depending what you mean by > > "heavy water". Either way, you'll need some fluency with > > GROMACS workflows and file types, so do all the general > > tutorial material you can find. If you'd done so, you might > > have realised that pdb2gmx is not really the tool for the > > job. > > > > Mark > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water clusters MD
Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say I don't need it. Ok may be topology file can be written by hand, but what about "gro" file? --- On Mon, 5/31/10, Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] water clusters MD > To: "Discussion list for GROMACS users" > Date: Monday, May 31, 2010, 10:55 AM > - Original Message - > From: Oleksandr > Date: Monday, May 31, 2010 18:48 > Subject: [gmx-users] water clusters MD > To: gmx-users@gromacs.org > > > Hi, > > I'm new user of Gromacs. There are plenty examples how > to do > > solvation study of various proteins. But I'd like to > "solvate" > > highly ordered heavy water clusters in box of light > water. At > > the first step when I execute "pdb2gmx -f > watercluster.pdb" I > > get an error no matter which model is chosen: > > > --- > > > > Fatal error: > > Atom H in residue HOH 4 not found in rtp entry with 3 > atoms > > while sorting atoms. Maybe > different protonation state. > > Remove this hydrogen or choose a > different > > protonation state. > > Option -ignh will ignore all > hydrogens in the input. > > > --- > > > > Can anybody help me how to solve this problem? > > You're using a tool for a different job. pdb2gmx builds a > topology file, mostly by constructing a [moleculetype] from > a polymer of repeating units. Your moleculetypes are > trivial, and at least one is already present in an .itp file > for use with #include. > > editconf and genbox make a box and fill it with generic > solvent. It will be simplest to either write your .top by > hand, or adapt an existing .top, depending what you mean by > "heavy water". Either way, you'll need some fluency with > GROMACS workflows and file types, so do all the general > tutorial material you can find. If you'd done so, you might > have realised that pdb2gmx is not really the tool for the > job. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water clusters MD
- Original Message - From: Oleksandr Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org > Hi, > I'm new user of Gromacs. There are plenty examples how to do > solvation study of various proteins. But I'd like to "solvate" > highly ordered heavy water clusters in box of light water. At > the first step when I execute "pdb2gmx -f watercluster.pdb" I > get an error no matter which model is chosen: > --- > > Fatal error: > Atom H in residue HOH 4 not found in rtp entry with 3 atoms > while sorting atoms. Maybe different protonation state. > Remove this hydrogen or choose a different > protonation state. > Option -ignh will ignore all hydrogens in the input. > --- > > Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by "heavy water". Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] water clusters MD
Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to "solvate" highly ordered heavy water clusters in box of light water. At the first step when I execute "pdb2gmx -f watercluster.pdb" I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? Thanks a lot Oleksandr -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
