Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?
On Tue, Dec 7, 2010 at 3:17 PM, Mark Abraham wrote: > On 8/12/2010 4:07 AM, J. Nathan Scott wrote: >> >> Hello all! I spent some time searching the archive and can't find an >> answer to this question. Is there a replacement for the -rtpo option >> for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am >> using) manual (pg 115) but does not seem to work, and yields the error >> "Invalid command line argument: -rtpo" when I try to use it >> >> I would basically like to have the OPLSAA aminoacids.rtp file in my >> working directory (which has some modified charges for the TRP >> residue) supersede the one in the Gromacs force field share directory. >> Is there a way to do this? >> >> So far I have resorted to copying the shared oplsaa.ff folder to my >> working directory and modifying the aminoacids.rtp file in that >> directory, and then selecting that directory to source my force field >> when I run pdb2gmx. > > This is the intended behaviour. Rather than modifying your installed > database, or having to mess with the GMXLIB environment variable, you can > copy the whole xx.ff directory into a local directory and have local > modifications. pdb2gmx reports clearly on stdout which directory(s) it is > (considering) using. > >> This of course works, but I have noted a peculiar >> behavior using this method. No matter whether I select force field 1, >> which is OPLSAA from my working directory, or force field 15, which is >> OPLSAA from the share directory, my topology file ends up with charges >> in the working directory oplsaa.ff folder's aminoacids.rtp file. Even >> when I select that pdb2gmx should use the share version, it is clearly >> still using the force field folder in my working directory. I >> confirmed this by renaming the aminoacids.rtp in the working directory >> file to aminoacids.rtp.bak, which produced the error "Could not find >> any files ending on '.rtp' in the force field directory 'oplsaa.ff'" > > That sounds very weird. I'd suggest you start a new working directory, copy > the oplsaa.ff over fresh, make the .rtp modifications and see if you can > reproduce the issue. If so, please file a Bugzilla. Thanks for your reply Mark. I have confirmed this behavior many times now, and so I have filed a Bugzilla report as you suggested. I did find a quick fix: as long as the copy of the .ff directory in the working directory is named something different than the copy in share/top then pdb2gmx seems to differentiate between the two perfectly well, as confirmed by the charges in the topology files it is generating. It is only when they are named the same thing (oplsaa.ff, for instance) that the force field selection problem happens. Perhaps the programmers assumed users would be smart enough to rename the modified force field directory? ;) Best Wishes, -Nathan > >> Can someone recommend a better method for what I am attempting to do? >> Also, is pdb2gmx's handling of force field directories appropriate? I >> had assumed that selecting the share version of a force field would >> force all the necessary files to be read from that share directory, >> but this is clearly not the case. > > It should be the case. > > Mark > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?
On 8/12/2010 4:07 AM, J. Nathan Scott wrote: Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to work, and yields the error "Invalid command line argument: -rtpo" when I try to use it I would basically like to have the OPLSAA aminoacids.rtp file in my working directory (which has some modified charges for the TRP residue) supersede the one in the Gromacs force field share directory. Is there a way to do this? So far I have resorted to copying the shared oplsaa.ff folder to my working directory and modifying the aminoacids.rtp file in that directory, and then selecting that directory to source my force field when I run pdb2gmx. This is the intended behaviour. Rather than modifying your installed database, or having to mess with the GMXLIB environment variable, you can copy the whole xx.ff directory into a local directory and have local modifications. pdb2gmx reports clearly on stdout which directory(s) it is (considering) using. This of course works, but I have noted a peculiar behavior using this method. No matter whether I select force field 1, which is OPLSAA from my working directory, or force field 15, which is OPLSAA from the share directory, my topology file ends up with charges in the working directory oplsaa.ff folder's aminoacids.rtp file. Even when I select that pdb2gmx should use the share version, it is clearly still using the force field folder in my working directory. I confirmed this by renaming the aminoacids.rtp in the working directory file to aminoacids.rtp.bak, which produced the error "Could not find any files ending on '.rtp' in the force field directory 'oplsaa.ff'" That sounds very weird. I'd suggest you start a new working directory, copy the oplsaa.ff over fresh, make the .rtp modifications and see if you can reproduce the issue. If so, please file a Bugzilla. Can someone recommend a better method for what I am attempting to do? Also, is pdb2gmx's handling of force field directories appropriate? I had assumed that selecting the share version of a force field would force all the necessary files to be read from that share directory, but this is clearly not the case. It should be the case. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?
Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to work, and yields the error "Invalid command line argument: -rtpo" when I try to use it I would basically like to have the OPLSAA aminoacids.rtp file in my working directory (which has some modified charges for the TRP residue) supersede the one in the Gromacs force field share directory. Is there a way to do this? So far I have resorted to copying the shared oplsaa.ff folder to my working directory and modifying the aminoacids.rtp file in that directory, and then selecting that directory to source my force field when I run pdb2gmx. This of course works, but I have noted a peculiar behavior using this method. No matter whether I select force field 1, which is OPLSAA from my working directory, or force field 15, which is OPLSAA from the share directory, my topology file ends up with charges in the working directory oplsaa.ff folder's aminoacids.rtp file. Even when I select that pdb2gmx should use the share version, it is clearly still using the force field folder in my working directory. I confirmed this by renaming the aminoacids.rtp in the working directory file to aminoacids.rtp.bak, which produced the error "Could not find any files ending on '.rtp' in the force field directory 'oplsaa.ff'" Can someone recommend a better method for what I am attempting to do? Also, is pdb2gmx's handling of force field directories appropriate? I had assumed that selecting the share version of a force field would force all the necessary files to be read from that share directory, but this is clearly not the case. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists