Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
Hi, I think that the terminal oxygen atoms should not be named OXT for the amber forcefields but rather OC1 and OC2. To check this look in the top folder at the ffamberXX.rtp file. Hope this helps Tom --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson [EMAIL PROTECTED] wrote: Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following error message: Warning: atom names in topology.top and coordinates.pdb don't match (OXT - O2) However, checking the actual files reveals that the atoms were initially named consistently. It seems that whenever we run various Gromacs programs (such as grompp or editconf), the OXT atom name is changed to O2. In other words, topology.top and coordinates.pdb both have the atom correctly named as OXT. It seems that Gromacs wants to substitute a 2 for the XT. Does anyone know why Gromacs does this? Is this due to a bug in the code or is there some environment variable that defines XT=2? Thanks, Bob Johnson ___ 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. On 6/13/07, TJ Piggot [EMAIL PROTECTED] wrote: Hi, I think that the terminal oxygen atoms should not be named OXT for the amber forcefields but rather OC1 and OC2. To check this look in the top folder at the ffamberXX.rtp file. Hope this helps Tom --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson [EMAIL PROTECTED] wrote: Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following error message: Warning: atom names in topology.top and coordinates.pdb don't match (OXT - O2) However, checking the actual files reveals that the atoms were initially named consistently. It seems that whenever we run various Gromacs programs (such as grompp or editconf), the OXT atom name is changed to O2. In other words, topology.top and coordinates.pdb both have the atom correctly named as OXT. It seems that Gromacs wants to substitute a 2 for the XT. Does anyone know why Gromacs does this? Is this due to a bug in the code or is there some environment variable that defines XT=2? Thanks, Bob Johnson ___ 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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 ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. you are welcome to submit a bugzilla, but for pdb2gmx this is the expected behavior. if you would like to change that you would have to edit database files. in principle naming should adhere to IUPAC/IUPAB standards (Biochemistry 9, 3471-3479 [1970]), but in practice there are at least four different naming schemes around only for hydrogens and other atoms (see http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl). It seems that the GROMACS scheme (which is derived from GROMOS force field) is correct for the terminal oxygens. Almost all programs are wrong as regards hydrogen naming. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
On 6/14/2007 1:14 AM, Erik Lindahl wrote: Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. Don't bother for now :-) This is because of a few old brain-dead choices in pdb2gmx, but we're working on replacing that completely, and then we'll be name-agnostic. The only thing I can say in our defense is that most other programs also push their own naming convention when generation hydrogens, etc. For instance, charmm will rename the resname of the first/last few atoms in each chain to NTER/CTER. Hi, Robert I am clueless why this topic has again made people upset about Gromacs. You may search for David Mathog in mailing list archive. e.g. http://www.gromacs.org/pipermail/gmx-users/2006-February/020087.html David, in the end, contributed some conversion script you might take a look. I admit that it is frustrated to add on more rules when I want to let pdb2gmx pass my PDB file. But when you are working with different force field, AMBER, CHARMM and OPLS-AA, like me, pdb2gmx will definitely have a dilemma to choose which atom instead of a fixed answer. Since, as you say, it is easy to change the atom name, why don't you do yourself? IMHO, it is rather to have a strict program which is faithful and rigid than to have an smart one which may induce errors. Of course, I believe Erik has a better idea to solve this problem. Cheers, Erik ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
I could understand if it was doing this within pdb2gmx or something that was constructing a topology file. I'm observing this behavior when using editconf to simply convert files to another format or apply box dimensions etc. Anyway, I submitted a bugzilla about it. This isn't such a big problem - make of it what you will. ;-) Bob On 6/13/07, Erik Lindahl [EMAIL PROTECTED] wrote: Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. Don't bother for now :-) This is because of a few old brain-dead choices in pdb2gmx, but we're working on replacing that completely, and then we'll be name-agnostic. The only thing I can say in our defense is that most other programs also push their own naming convention when generation hydrogens, etc. For instance, charmm will rename the resname of the first/last few atoms in each chain to NTER/CTER. Cheers, Erik ___ 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 ___ 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
[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following error message: Warning: atom names in topology.top and coordinates.pdb don't match (OXT - O2) However, checking the actual files reveals that the atoms were initially named consistently. It seems that whenever we run various Gromacs programs (such as grompp or editconf), the OXT atom name is changed to O2. In other words, topology.top and coordinates.pdb both have the atom correctly named as OXT. It seems that Gromacs wants to substitute a 2 for the XT. Does anyone know why Gromacs does this? Is this due to a bug in the code or is there some environment variable that defines XT=2? Thanks, Bob Johnson ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
Robert Johnson wrote: Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following error message: Warning: atom names in topology.top and coordinates.pdb don't match (OXT - O2) However, checking the actual files reveals that the atoms were initially named consistently. It seems that whenever we run various Gromacs programs (such as grompp or editconf), the OXT atom name is changed to O2. In other words, topology.top and coordinates.pdb both have the atom correctly named as OXT. It seems that Gromacs wants to substitute a 2 for the XT. Does anyone know why Gromacs does this? Is this due to a bug in the code or is there some environment variable that defines XT=2? Thanks, Bob Johnson ___ AFAIK only pdb2gmx renames atoms. If you have an example that proves otherwise it's worth a bugzilla. The pdb has to be correctly formatted of course. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
