[gmx-users] g_select problem
Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat and here is my select.dat: waterO = water and name OW and z30 and z70; close = water0 and within 0.4 of group Protein; close it failed with messages: Reading file ../md.tpr, VERSION 4.6.3 (single precision) Reading file ../md.tpr, VERSION 4.6.3 (single precision) selection parser: syntax error selection parser: invalid selection 'waterO = water and name OW and z30 and z70' I am just wondering, is there anything wrong with my syntax? thank you very much. best Albert -- 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] g_select problem
Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. On Sat, Sep 28, 2013 at 1:00 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat and here is my select.dat: waterO = water and name OW and z30 and z70; close = water0 and within 0.4 of group Protein; close it failed with messages: Reading file ../md.tpr, VERSION 4.6.3 (single precision) Reading file ../md.tpr, VERSION 4.6.3 (single precision) selection parser: syntax error selection parser: invalid selection 'waterO = water and name OW and z30 and z70' I am just wondering, is there anything wrong with my syntax? thank you very much. best Albert -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_select problem
On 09/28/2013 09:42 AM, rajat desikan wrote: Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. Hi Rajat: thanks a lot for such kind and helpful comments. It works now. I run it by command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat -os size.xvg -oc cfrac.xvg -oi index.dat I am trying to make density of the water molecules inside my protein by g_density: g_density_mpi -f ../md_pbc_center.xtc -s ../md.tpr -ei density.ndx -o density.xvg -n density.ndx but it asked me which water molecules I would like to make. Do you have any idea how to do this correctly? thank you very much. best Albert -- 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] g_select problem
Hello: I am trying to calculate the number of water molecules within 3 A of a resid 51, and here is my command: g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat here is my selection.dat: waterO = name T3P and name O; close = waterO and within 0.3 of resnr 51; close the command run without errors, but I noticed that the number of water molecules in the output file are all 0. When I visualize each frame, I observe a lot of water molecules within the defined region. Does anybody have any idea what's the problem? thx Albert -- 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] g_select problem
Simplify your condition gradually and find out which bit is wrong! Mark On Wed, Aug 21, 2013 at 4:13 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to calculate the number of water molecules within 3 A of a resid 51, and here is my command: g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat here is my selection.dat: waterO = name T3P and name O; close = waterO and within 0.3 of resnr 51; close the command run without errors, but I noticed that the number of water molecules in the output file are all 0. When I visualize each frame, I observe a lot of water molecules within the defined region. Does anybody have any idea what's the problem? thx Albert -- 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 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] g_select problem
Hello Mark: thanks for kind advices. I checked my residues number carefully, and I didn't find anything wrong. However, I am not sure whether the syntax of my selection.dat is all right or not, since the documentation for this option is not well clarified. thank you very much Albert On 08/21/2013 04:35 PM, Mark Abraham wrote: Simplify your condition gradually and find out which bit is wrong! 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
Re: [gmx-users] g_select problem
If that is really your selection, you are trying to select atoms that have both name T3P and O, which is clearly impossible, so nothing gets selected. Best regards, Teemu On Aug 21, 2013 5:13 PM, Albert mailmd2...@gmail.com wrote: Hello: I am trying to calculate the number of water molecules within 3 A of a resid 51, and here is my command: g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat here is my selection.dat: waterO = name T3P and name O; close = waterO and within 0.3 of resnr 51; close the command run without errors, but I noticed that the number of water molecules in the output file are all 0. When I visualize each frame, I observe a lot of water molecules within the defined region. Does anybody have any idea what's the problem? thx Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] g_select problem
but actually the water name in my system IS T3P and the atom name in the water model is O. I've double checked for this. thx Albert On 08/21/2013 04:59 PM, Teemu Murtola wrote: If that is really your selection, you are trying to select atoms that have both name T3P and O, which is clearly impossible, so nothing gets selected. Best regards, Teemu -- 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] g_select problem
On 8/21/13 11:02 AM, Albert wrote: but actually the water name in my system IS T3P and the atom name in the water model is O. I've double checked for this. Your selection, as Teemu says, is calling for *atoms* named T3P that are also *atoms* named O, which is clearly impossible. The *residue* name is T3P. -Justin thx Albert On 08/21/2013 04:59 PM, Teemu Murtola wrote: If that is really your selection, you are trying to select atoms that have both name T3P and O, which is clearly impossible, so nothing gets selected. Best regards, Teemu -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_select problem
On 08/21/2013 05:06 PM, Justin Lemkul wrote: Your selection, as Teemu says, is calling for *atoms* named T3P that are also *atoms* named O, which is clearly impossible. The *residue* name is T3P. -Justin I see. thanks a lot for clearly pointing out. I changed it into resname T3P and it works very well now. thanks all you guys. best Albert -- 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] g_select problem
... which is why simplifying your predicate would have helped you identify which part was wrong. Once you actually try close = name T3P; close and see that you get no atoms, your error becomes much easier to see! Also faster than emailing ;-) Mark On Wed, Aug 21, 2013 at 4:46 PM, Albert mailmd2...@gmail.com wrote: Hello Mark: thanks for kind advices. I checked my residues number carefully, and I didn't find anything wrong. However, I am not sure whether the syntax of my selection.dat is all right or not, since the documentation for this option is not well clarified. thank you very much Albert On 08/21/2013 04:35 PM, Mark Abraham wrote: Simplify your condition gradually and find out which bit is wrong! 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 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] g_select problem (Invalid command line argument:)
Hi Leila, You didn't enclose your selection string, you enclosed some words in your selection string. g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select Close to Protein 'resname' 'SOL' and within 0.25 of group 'Protein' g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select 'Close to Protein resname SOL and within 0.25 of group Protein' Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] g_select problem (Invalid command line argument:)
On 08/03/12, leila karami karami.lei...@gmail.com wrote: Dear Justin Thanks for your reply. As you said You need to enclose your selection string within ' ' so it is interpreted as a single string. , I enclosed my selection string: g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select Close to Protein 'resname' 'SOL' and within 0.25 of group 'Protein' You've enclosed each word of your selection string in its own set of single quotes. You need to enclose the whole of your selection string - including the name of the selection - in one set of single quotes. This forces your shell to pass the whole string as the argument to -select. Normally the shell breaks up the words before the tool you are using gets a look at them. Mark But, unfortunately, Program g_select, VERSION 4.5.1 Source code file: statutil.c, line: 819 Invalid command line argument: SOL If I'm wrong in using selection string above, please correct it. Best regards. -- 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] g_select problem (Invalid command line argument:)
Dear gromacs users My system contains protein and water molecules. I want to use g_select to obtain residue number of water molecules being within 0.35 nm of protein. My index file is as follows: [ Protein ] [SOL] When I use g_select -f *.xtc -s *.tpr -n index.ndx -oi -select Close to Protein resname SOL and within 0.35 of group Protein I encountered : Program g_select, VERSION 4.5.1 Source code file: statutil.c, line: 819 Invalid command line argument: SOL Why? How to fix it? Any help will highly appreciated. -- 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] g_select problem (Invalid command line argument:)
leila karami wrote: Dear gromacs users My system contains protein and water molecules. I want to use g_select to obtain residue number of water molecules being within 0.35 nm of protein. My index file is as follows: [ Protein ] [SOL] When I use g_select -f *.xtc -s *.tpr -n index.ndx -oi -select Close to Protein resname SOL and within 0.35 of group Protein I encountered : Program g_select, VERSION 4.5.1 Source code file: statutil.c, line: 819 Invalid command line argument: SOL Why? How to fix it? You need to enclose your selection string within ' ' so it is interpreted as a single string. As it stands, the words resname, SOL, and, etc are being interpreted as arguments, which they are not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] g_select problem (Invalid command line argument:)
Dear Justin Thanks for your reply. As you said You need to enclose your selection string within ' ' so it is interpreted as a single string. , I enclosed my selection string: g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select Close to Protein 'resname' 'SOL' and within 0.25 of group 'Protein' But, unfortunately, Program g_select, VERSION 4.5.1 Source code file: statutil.c, line: 819 Invalid command line argument: SOL If I'm wrong in using selection string above, please correct it. Best regards. -- 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
