[gmx-users] editconf displays incorrect mass of input, GROMACS version 4.5.4
Dear Gromacs users, Please somebody help . editconf computs the incorrect value of mass of input. I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp. The mass of input should be 15.99940 but it showing 222. Please help me whether this is bug or something wrong with my GROMACS. Its GROMACS version 4.5.4. I tested for just 1 atom to see error I have just 1 atom in my pdb so only on in .rtp too A.pdb CRYST1 12.000 12.000 12.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 O ENDMDL TER RM.rtp [ AOT ] ; [ atoms ] OS1 O2L -0.6000 1 [ bonds ] atomtypes.atp NTL 14.007000 ; ammonium nitrogen NH3L 14.007000 ; nitrogen phosphatidylethanolamine OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen OSLP 15.999400 ; Phosphate oxygen, to avoid conflict with methylacetate type O O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen PL 30.974000 ; phosphorus SL 32.06 ; Sulfate sulfur SOD 22.989770 ; Sodium Ion MG 24.305000 ; Magnesium Ion OUTPUT OF editconf Volume of input 125 (nm^3) Mass of input 222.295 (a.m.u.) This is incorrect, even to much incorrect. It should be 15.40 Density of input 2.95304 (g/l) Scaling all box vectors by 0.143468 new system size : 0.000 0.000 0.000 shift : 2.141 2.141 2.141 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00 (nm^3) -- 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] editconf displays incorrect mass of input, GROMACS version 4.5.4
On 10/30/13 2:34 PM, Hari Pandey wrote: Dear Gromacs users, Please somebody help . editconf computs the incorrect value of mass of input. I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp. The mass of input should be 15.99940 but it showing 222. Please help me whether this is bug or something wrong with my GROMACS. Its GROMACS version 4.5.4. I tested for just 1 atom to see error I have just 1 atom in my pdb so only on in .rtp too A.pdb CRYST1 12.000 12.000 12.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 OS1AOT 151 7.820 -5.791 -0.815 1.00 0.00 O ENDMDL TER RM.rtp [ AOT ] ; [ atoms ] OS1 O2L -0.6000 1 [ bonds ] atomtypes.atp NTL 14.007000 ; ammonium nitrogen NH3L14.007000 ; nitrogen phosphatidylethanolamine OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen OSLP15.999400 ; Phosphate oxygen, to avoid conflict with methylacetate type O O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen PL 30.974000 ; phosphorus SL 32.06 ; Sulfate sulfur SOD 22.989770 ; Sodium Ion MG 24.305000 ; Magnesium Ion OUTPUT OF editconf Volume of input 125 (nm^3) Massof input 222.295 (a.m.u.) This is incorrect, even to much incorrect. It should be 15.40 Density of input 2.95304 (g/l) Scaling all box vectors by 0.143468 new system size : 0.000 0.000 0.000 shift : 2.141 2.141 2.141 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00 (nm^3) I cannot reproduce the problem with 4.6.3. I get correct output: Volume of input 1.728 (nm^3) Massof input 15.9994 (a.m.u.) Density of input 15.3748 (g/l) Scaling all box vectors by 0.248658 new system size : 0.000 0.000 0.000 shift : 2.326 2.480 2.480 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00 (nm^3) -Justin -- == 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] editconf: Invalid command line argument: –f
Hi Jonathan, I suspect the dash is not of the right kind. Did you by chance copy/paste the command? Did you try typing it? Cheers, Tsjerk On Sat, Jul 13, 2013 at 12:03 AM, Jonathan Saboury jsab...@gmail.comwrote: I am following Tutorial 1 from https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro but I get the error: Program editconf, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: –f Here are the files I am currently using: http://www.sendspace.com/file/a2twvx What is the problem? Thanks! -Jonathan -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] editconf: Invalid command line argument: –f
I am following Tutorial 1 from https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro but I get the error: Program editconf, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: –f Here are the files I am currently using: http://www.sendspace.com/file/a2twvx What is the problem? Thanks! -Jonathan -- 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] editconf- pdb to gro format
Hi all, I am trying to produce gro file from PDB file using editconf. Here is the pdb file HETATM1 C 0.672 -0.000 0.000 C HETATM2 C -0.672 -0.000 0.000 C HETATM3 H 1.238 -0.928 0.000 H HETATM4 H 1.238 0.928 0.000 H HETATM5 H -1.238 -0.928 0.000 H HETATM6 H -1.238 0.928 0.000 H Then I use: editconf -f X.pdb -o X.gro But the go file seems no to be correct 6 0 C1 0.067 -0.000 0.000 0 C2 -0.067 -0.000 0.000 0 H3 0.124 -0.093 0.000 0 H4 0.124 0.093 0.000 0 H5 -0.124 -0.093 0.000 0 H6 -0.124 0.093 0.000 0.0 0.0 0.0 Can anyone please help why this is happening? Thank you! -- Thanks, J. N. -- 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] editconf- pdb to gro format
On 4/1/13 7:22 PM, Juliette N. wrote: Hi all, I am trying to produce gro file from PDB file using editconf. Here is the pdb file HETATM1 C 0.672 -0.000 0.000 C HETATM2 C -0.672 -0.000 0.000 C HETATM3 H 1.238 -0.928 0.000 H HETATM4 H 1.238 0.928 0.000 H HETATM5 H -1.238 -0.928 0.000 H HETATM6 H -1.238 0.928 0.000 H Then I use: editconf -f X.pdb -o X.gro But the go file seems no to be correct 6 0 C1 0.067 -0.000 0.000 0 C2 -0.067 -0.000 0.000 0 H3 0.124 -0.093 0.000 0 H4 0.124 0.093 0.000 0 H5 -0.124 -0.093 0.000 0 H6 -0.124 0.093 0.000 0.0 0.0 0.0 Can anyone please help why this is happening? And what exactly is wrong with it? You have no residue numbers or names in the input .pdb file, so none appear in the .gro file. The coordinates have been correctly transformed from Angstrom to nm within the limit of precision. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] editconf- pdb to gro format
Hi Justin I tried several residue names, 1Ethylene, 1Eth but editconf says: Program editconf, VERSION 4.5.4 Source code file: pdbio.c, line: 446 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What would be the correct format of pdb that is readable? Here is the pdb: 1Eth1 C 0.672 -0.000 0.000 C 1Eth2 C -0.672 -0.000 0.000 C 1Eth3 H 1.238 -0.928 0.000 H 1Eth4 H 1.238 0.928 0.000 H 1Eth5 H -1.238 -0.928 0.000 H 1Eth6 H -1.238 0.928 0.000 H Thanks On 1 April 2013 20:06, Justin Lemkul jalem...@vt.edu wrote: On 4/1/13 7:22 PM, Juliette N. wrote: Hi all, I am trying to produce gro file from PDB file using editconf. Here is the pdb file HETATM1 C 0.672 -0.000 0.000 C HETATM2 C -0.672 -0.000 0.000 C HETATM3 H 1.238 -0.928 0.000 H HETATM4 H 1.238 0.928 0.000 H HETATM5 H -1.238 -0.928 0.000 H HETATM6 H -1.238 0.928 0.000 H Then I use: editconf -f X.pdb -o X.gro But the go file seems no to be correct 6 0 C1 0.067 -0.000 0.000 0 C2 -0.067 -0.000 0.000 0 H3 0.124 -0.093 0.000 0 H4 0.124 0.093 0.000 0 H5 -0.124 -0.093 0.000 0 H6 -0.124 0.093 0.000 0.0 0.0 0.0 Can anyone please help why this is happening? And what exactly is wrong with it? You have no residue numbers or names in the input .pdb file, so none appear in the .gro file. The coordinates have been correctly transformed from Angstrom to nm within the limit of precision. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Thanks, J. N. -- 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] editconf- pdb to gro format
On 4/1/13 8:55 PM, Juliette N. wrote: Hi Justin I tried several residue names, 1Ethylene, 1Eth but editconf says: Program editconf, VERSION 4.5.4 Source code file: pdbio.c, line: 446 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What would be the correct format of pdb that is readable? Here is the pdb: Google PDB format. -Justin 1Eth1 C 0.672 -0.000 0.000 C 1Eth2 C -0.672 -0.000 0.000 C 1Eth3 H 1.238 -0.928 0.000 H 1Eth4 H 1.238 0.928 0.000 H 1Eth5 H -1.238 -0.928 0.000 H 1Eth6 H -1.238 0.928 0.000 H Thanks On 1 April 2013 20:06, Justin Lemkul jalem...@vt.edu wrote: On 4/1/13 7:22 PM, Juliette N. wrote: Hi all, I am trying to produce gro file from PDB file using editconf. Here is the pdb file HETATM1 C 0.672 -0.000 0.000 C HETATM2 C -0.672 -0.000 0.000 C HETATM3 H 1.238 -0.928 0.000 H HETATM4 H 1.238 0.928 0.000 H HETATM5 H -1.238 -0.928 0.000 H HETATM6 H -1.238 0.928 0.000 H Then I use: editconf -f X.pdb -o X.gro But the go file seems no to be correct 6 0 C1 0.067 -0.000 0.000 0 C2 -0.067 -0.000 0.000 0 H3 0.124 -0.093 0.000 0 H4 0.124 0.093 0.000 0 H5 -0.124 -0.093 0.000 0 H6 -0.124 0.093 0.000 0.0 0.0 0.0 Can anyone please help why this is happening? And what exactly is wrong with it? You have no residue numbers or names in the input .pdb file, so none appear in the .gro file. The coordinates have been correctly transformed from Angstrom to nm within the limit of precision. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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] editconf not centering, and it is cutting off my molecule
Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. Any input is appreciated. Thank you! Xu Dong Huang Chemical Biochemical Engineering-Undergraduate Researcher Rutgers School of Engineering xudo...@eden.rutgers.edu -- 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] editconf not centering, and it is cutting off my molecule
On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. editconf builds boxes from the coordinate origin so that there are never negative coordinates. It should be able to deal with those coordinates, equally shifted, which it appears they were. Can you provide images of what's going on? I don't clearly understand what's wrong. What do you mean by cut off? Nonexistent? Incorrectly placed? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] editconf not centering, and it is cutting off my molecule
Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. editconf builds boxes from the coordinate origin so that there are never negative coordinates. It should be able to deal with those coordinates, equally shifted, which it appears they were. Can you provide images of what's going on? I don't clearly understand what's wrong. What do you mean by cut off? Nonexistent? Incorrectly placed? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] editconf not centering, and it is cutting off my molecule
On 12/31/12 5:40 PM, Xu Dong Huang wrote: Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening. Is your .gro file valid? Specifically, does the second line of the input file specify the correct number of atoms? Does the output file have the same number of atoms as the input? That is the only reason I know of for a file being truncated. -Justin Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695 2star O2 179 12.421 24.461 16.695 2star O2 180 12.421 24.891 16.695 2star O2 181 12.421 25.321 16.695 2star O2 182 12.421 25.751 16.695 2star O2 183 12.421 26.181 16.695 Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? All i can see in VMD is my negative axis part of the molecule beads are cut off. editconf builds boxes from the coordinate origin so that there are never negative coordinates. It should be able to deal with those coordinates, equally shifted, which it appears they were. Can you provide images of what's going on? I don't clearly understand what's wrong. What do you mean by cut off? Nonexistent? Incorrectly placed? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] editconf not centering, and it is cutting off my molecule
Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1starO12 0.430 0.000 0.000 1starO13 0.860 0.000 0.000 1starO14 1.290 0.000 0.000 1starO15 1.720 0.000 0.000 1starO16 2.150 0.000 0.000 1starO17 2.580 0.000 0.000 1starO18 3.010 0.000 0.000 1starO19 3.440 0.000 0.000 1starO1 10 3.870 0.000 0.000 1starO1 11 4.300 0.000 0.000 1starO1 12 4.730 0.000 0.000 1starO1 13 5.160 0.000 0.000 1starO1 14 5.590 0.000 0.000 1starO1 15 6.020 0.000 0.000 1starO1 16 6.450 0.000 0.000 1starO1 17 6.880 0.000 0.000 1starO1 18 7.310 0.000 0.000 1starO1 19 7.740 0.000 0.000 1starO1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O1 11 16.221 11.921 16.195 1star O1 12 16.651 11.921 16.195 1star O1 13 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... Another reason why I think my .gro is valid is that when I editconf, it says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is valid? Please let me know, thank you. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:40 PM, Xu Dong Huang xudo...@eden.rutgers.edu wrote: Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: **original .gro coordinates: 1star O1 170 0.000 -8.170 0.000 1star O1 171 0.000 -8.600 0.000 2star O2 172 0.000 -9.030 0.000 2star O2 173 0.000 -9.460 0.000 2star O2 174 0.000 -9.890 0.000 2star O2 175 0.000 -10.320 0.000 2star O2 176 0.000 -10.750 0.000 2star O2 177 0.000 -11.180 0.000 2star O2 178 0.000 -11.610 0.000 2star O2 179 0.000 -12.040 0.000 2star O2 180 0.000 -12.470 0.000 2star O2 181 0.000 -12.900 0.000 2star O2 182 0.000 -13.330 0.000 2star O2 183 0.000 -13.760 0.000 *new .gro coordinates: 1star O1 169 12.421 4.681 16.695 1star O1 170 12.421 4.251 16.695 1star O1 171 12.421 3.821 16.695 2star O2 172 12.421 3.391 16.695 2star O2 173 12.421 2.961 16.695 2star O2 174 12.421 2.531 16.695 2star O2 175 12.421 22.741 16.695 2star O2 176 12.421 23.171 16.695 2star O2 177 12.421 23.601 16.695 2star O2 178 12.421 24.031 16.695
Re: [gmx-users] editconf not centering, and it is cutting off my molecule
On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1star O13 0.860 0.000 0.000 1star O14 1.290 0.000 0.000 1star O15 1.720 0.000 0.000 1star O16 2.150 0.000 0.000 1star O17 2.580 0.000 0.000 1star O18 3.010 0.000 0.000 1star O19 3.440 0.000 0.000 1star O1 10 3.870 0.000 0.000 1star O1 11 4.300 0.000 0.000 1star O1 12 4.730 0.000 0.000 1star O1 13 5.160 0.000 0.000 1star O1 14 5.590 0.000 0.000 1star O1 15 6.020 0.000 0.000 1star O1 16 6.450 0.000 0.000 1star O1 17 6.880 0.000 0.000 1star O1 18 7.310 0.000 0.000 1star O1 19 7.740 0.000 0.000 1star O1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O111 16.221 11.921 16.195 1star O112 16.651 11.921 16.195 1star O113 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... Another reason why I think my .gro is valid is that when I editconf, it says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is valid? Please let me know, thank you. Yes, those files should be fine. Can you send me the two coordinate files (off-list) so I can investigate what's going on? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] editconf not centering, and it is cutting off my molecule
Ok I sent it. Let me know if you did not receive them. Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1star O13 0.860 0.000 0.000 1star O14 1.290 0.000 0.000 1star O15 1.720 0.000 0.000 1star O16 2.150 0.000 0.000 1star O17 2.580 0.000 0.000 1star O18 3.010 0.000 0.000 1star O19 3.440 0.000 0.000 1star O1 10 3.870 0.000 0.000 1star O1 11 4.300 0.000 0.000 1star O1 12 4.730 0.000 0.000 1star O1 13 5.160 0.000 0.000 1star O1 14 5.590 0.000 0.000 1star O1 15 6.020 0.000 0.000 1star O1 16 6.450 0.000 0.000 1star O1 17 6.880 0.000 0.000 1star O1 18 7.310 0.000 0.000 1star O1 19 7.740 0.000 0.000 1star O1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O1 11 16.221 11.921 16.195 1star O1 12 16.651 11.921 16.195 1star O1 13 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... Another reason why I think my .gro is valid is that when I editconf, it says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the .gro is valid? Please let me know, thank you. Yes, those files should be fine. Can you send me the two coordinate files (off-list) so I can investigate what's going on? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] editconf not centering, and it is cutting off my molecule
On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1star O13 0.860 0.000 0.000 1star O14 1.290 0.000 0.000 1star O15 1.720 0.000 0.000 1star O16 2.150 0.000 0.000 1star O17 2.580 0.000 0.000 1star O18 3.010 0.000 0.000 1star O19 3.440 0.000 0.000 1star O1 10 3.870 0.000 0.000 1star O1 11 4.300 0.000 0.000 1star O1 12 4.730 0.000 0.000 1star O1 13 5.160 0.000 0.000 1star O1 14 5.590 0.000 0.000 1star O1 15 6.020 0.000 0.000 1star O1 16 6.450 0.000 0.000 1star O1 17 6.880 0.000 0.000 1star O1 18 7.310 0.000 0.000 1star O1 19 7.740 0.000 0.000 1star O1 20 8.170 0.000 0.000 ... and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, ) star polymer 201 1starO41 11.921 11.921 16.195 1star O1 2 12.351 11.921 16.195 1star O1 3 12.781 11.921 16.195 1star O1 4 13.211 11.921 16.195 1star O1 5 13.641 11.921 16.195 1star O1 6 14.071 11.921 16.195 1star O1 7 14.501 11.921 16.195 1star O1 8 14.931 11.921 16.195 1starO19 15.361 11.921 16.195 1starO1 10 15.791 11.921 16.195 1star O111 16.221 11.921 16.195 1star O112 16.651 11.921 16.195 1star O113 17.081 11.921 16.195 1starO1 14 17.511 11.921 16.195 1starO1 15 17.941 11.921 16.195 ... The issue here is spacing. The files have tabs in them, which break the mandatory alignment for a .gro file. The atoms did not display because VMD could not correctly read the coordinate fields. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] editconf do not center protein
Hi everybody, I want to put my protein in a box with the command: editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2logErr 1logOut and add solvent afterwards with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2logErr 1logOut But when I look at it I see that the protein is not in the center of the box. Why? There are no errors or warnings in the log files. Best, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] editconf do not center protein
On 6/29/12 4:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to put my protein in a box with the command: editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2logErr 1logOut and add solvent afterwards with: genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro 2logErr 1logOut But when I look at it I see that the protein is not in the center of the box. Why? There are no errors or warnings in the log files. The protein is centered, but the representation of the unit cell is probably not what you expect. The box will be represented by a triclinic unit cell unless re-wrapped with trjconv -pbc mol -ur compact (which requires a .tpr file). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] editconf and g_editconf confusion
Hi, Can anyone please tell me what is the difference between the commands editconf and g_editconf? If there is no difference then why do some systems recognize g_editconf but not editconf? -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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] editconf and g_editconf confusion
On 5/11/12 7:40 PM, Nitin Agrawal wrote: Hi, Can anyone please tell me what is the difference between the commands editconf and g_editconf? If there is no difference then why do some systems recognize g_editconf but not editconf? There is no difference. g_editconf is just editconf but with a prefix. Some Linux distributions (like Fedora) have Gromacs packages that have such nomenclature. I believe the reason this was done was to avoid potential conflicts between the names of certain tools and other programs that may be installed on the system. -Justin -- Justin A. Lemkul, Ph.D. 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
Re: [gmx-users] editconf and g_editconf confusion
Thank you for your clarification. On Sat, May 12, 2012 at 2:51 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/11/12 7:40 PM, Nitin Agrawal wrote: Hi, Can anyone please tell me what is the difference between the commands editconf and g_editconf? If there is no difference then why do some systems recognize g_editconf but not editconf? There is no difference. g_editconf is just editconf but with a prefix. Some Linux distributions (like Fedora) have Gromacs packages that have such nomenclature. I believe the reason this was done was to avoid potential conflicts between the names of certain tools and other programs that may be installed on the system. -Justin -- ==**== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Regards, Nitin Agrawal, Master's Student (Bioinformatics) University of Turku,Finland B.Tech (Biotechnology) National Institute of Technology,Durgapur,India Blog:http://notjustanyotherblog.blogspot.com/ -- 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] editconf -d
Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? Best Regards Sara -- 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] editconf -d
mohammad agha wrote: Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? If you've got a box built, what's the need for -d? The purpose of setting a value with -d is to define a unit cell around a solute such that it does not interact with its periodic image during the simulation. The value is, to some extent, controlled by the cutoff values used during MD. -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] editconf -d
Dear Prof. I have a system consists of 500 surfactants + 61000 water beads + 500 ion in martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know the best quantity for -d option in editconf program to prevent from artificial forces, please? Best Regards Sara -- 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] editconf
Hi, when I choose different box types and draw them by Pymol, I see no visual difference between them. At least cubic must be different from the others. What is the reason for this? best wishes -- 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] editconf
Hi Mustafa, Check the section on periodic boundary conditions in the manual. Also be sure to use 'show cell' in Pymol to display the triclinic unit cell. That will show you the differences. Besides that, do a direct comparison of the lines encoding the boxes; either the last line of a .gro fil, or the line starting with 'CRYST1' in a.pdb file. Cheers, Tsjerk On Thu, Nov 4, 2010 at 1:23 AM, mustafa bilsel mfbil...@gmail.com wrote: Hi, when I choose different box types and draw them by Pymol, I see no visual difference between them. At least cubic must be different from the others. What is the reason for this? best wishes -- 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 -- 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] editconf
Hello, I am trying to rotate my protein in my simulation box (solvent molecules are there as well). I issue the following command: editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 I select my group (protein) in the first group selection prompt and whole system as output in the second prompt. However, in the output file the whole system is rotated rather than protein only. Also, despite the -box switch used, the dimensions of the box changes. Is there any ideas on what I am missing in my procedure? Regards, Paymon -- 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] editconf
On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: Hello, I am trying to rotate my protein in my simulation box (solvent molecules are there as well). I issue the following command: editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 I select my group (protein) in the first group selection prompt and whole system as output in the second prompt. However, in the output file the whole system is rotated rather than protein only. Also, despite the -box switch used, the dimensions of the box changes. Is there any ideas on what I am missing in my procedure? editconf can't rotate the solute with solvent present - what would you like it to do about the voids and clashes that would be created? Do your rotation before you solvate. 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] editconf
Payman Pirzadeh wrote: After rotation, wouldn't a minimization with very very small steps solve the problem? If any atoms overlap, you can't count on this working. It would be hit or miss. The proper way to build the system would be to orient the solute, then fill the box with solvent. Far more reliable. -Justin Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: Hello, I am trying to rotate my protein in my simulation box (solvent molecules are there as well). I issue the following command: editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 I select my group (protein) in the first group selection prompt and whole system as output in the second prompt. However, in the output file the whole system is rotated rather than protein only. Also, despite the -box switch used, the dimensions of the box changes. Is there any ideas on what I am missing in my procedure? editconf can't rotate the solute with solvent present - what would you like it to do about the voids and clashes that would be created? Do your rotation before you solvate. Mark -- 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
Re: [gmx-users] editconf
On 19/10/2010 12:22 PM, Payman Pirzadeh wrote: After rotation, wouldn't a minimization with very very small steps solve the problem? Only if the solute surface was very close to being symmetric about the rotation axis. Since that never happens, editconf doesn't even have the ability to try. Mark Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: Hello, I am trying to rotate my protein in my simulation box (solvent molecules are there as well). I issue the following command: editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 I select my group (protein) in the first group selection prompt and whole system as output in the second prompt. However, in the output file the whole system is rotated rather than protein only. Also, despite the -box switch used, the dimensions of the box changes. Is there any ideas on what I am missing in my procedure? editconf can't rotate the solute with solvent present - what would you like it to do about the voids and clashes that would be created? Do your rotation before you solvate. 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] editconf
Dear Mark and Justin, Thanks for very informative comments. I'll try to rotate and then solvate. Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 12:22 PM, Payman Pirzadeh wrote: After rotation, wouldn't a minimization with very very small steps solve the problem? Only if the solute surface was very close to being symmetric about the rotation axis. Since that never happens, editconf doesn't even have the ability to try. Mark Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: Hello, I am trying to rotate my protein in my simulation box (solvent molecules are there as well). I issue the following command: editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 I select my group (protein) in the first group selection prompt and whole system as output in the second prompt. However, in the output file the whole system is rotated rather than protein only. Also, despite the -box switch used, the dimensions of the box changes. Is there any ideas on what I am missing in my procedure? editconf can't rotate the solute with solvent present - what would you like it to do about the voids and clashes that would be created? Do your rotation before you solvate. 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
[gmx-users] editconf
Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the minimizationRun editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? Thank you in advance, Abdullah -- 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] editconf
abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1) 3. run gromp and mdrun for the minimization 4. Run editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines. -Justin Thank you in advance, Abdullah -- 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/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] editconf
-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1) 3. run gromp and mdrun for the minimization use mdrun -c . It will give you the required pdb file Chandan 4. Run editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines. -Justin Thank you in advance, Abdullah -- 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/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] editconf
- Original Message - From: abdullah ahmed abdullah_renk_ah...@hotmail.com Date: Saturday, August 14, 2010 1:05 Subject: [gmx-users] editconf To: gmx gmx-users@gromacs.org --- | Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: - Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) That's not quite the purpose of pdb2gmx. pdb2gmx generates the molecular topology in the .top file, and sanitizes the contents of the coordinate file, *by default* writing a .gro file. You could write this file in another format if you chose. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File - Run editconf to define the box (editconf -d 1) - run gromp and mdrun for the minimization - Run editconf to re-convert back to pdb You can use mdrun -c confout.pdb to do this last step directly. Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? I can't imagine what you mean. Did you use editconf on the .xtc or .trr file? In future, it's always a good idea to include your actual commands via copy-and-paste, else we are reduced to guessing whether you've done various things right or wrong, and that wastes our time and might not get you the help you need :-) Here, a small sample of the unrelated information might also have helped us understand the issue. 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] editconf/genbox: molecular complex outside simulation box
thanks. things are getting clearer and life's going a little easier, now. Justin A. Lemkul schrieb: dur...@zib.de wrote: hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p complex.top but when viewing the system of the resulting file (outfile.pdb), parts of the molecular complex turn out to be outside the box, although the box is obviously large enough. the complex is not centered, whether i use -c or not. i've tried several water models (tip4p, ffamber_tip3p) and all box shapes such as an octahedron, dodecah., cube, triclinic. the cubic one is the only one to result in a properly centered complex. but i prefer to use other box types. does anyone have an idea of the stage at which to search the cause for that problem? thanks a lot and regards This is just a visualization artifact. See, for instance: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions You can correct it by using trjconv (once you have assembled a .tpr file): trjconv -s *.tpr -f outfile.pdb -pbc mol -ur compact -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/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] editconf/genbox: molecular complex outside simulation box
hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p complex.top but when viewing the system of the resulting file (outfile.pdb), parts of the molecular complex turn out to be outside the box, although the box is obviously large enough. the complex is not centered, whether i use -c or not. i've tried several water models (tip4p, ffamber_tip3p) and all box shapes such as an octahedron, dodecah., cube, triclinic. the cubic one is the only one to result in a properly centered complex. but i prefer to use other box types. does anyone have an idea of the stage at which to search the cause for that problem? thanks a lot and 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/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] editconf/genbox: molecular complex outside simulation box
dur...@zib.de wrote: hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p complex.top but when viewing the system of the resulting file (outfile.pdb), parts of the molecular complex turn out to be outside the box, although the box is obviously large enough. the complex is not centered, whether i use -c or not. i've tried several water models (tip4p, ffamber_tip3p) and all box shapes such as an octahedron, dodecah., cube, triclinic. the cubic one is the only one to result in a properly centered complex. but i prefer to use other box types. does anyone have an idea of the stage at which to search the cause for that problem? thanks a lot and regards This is just a visualization artifact. See, for instance: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions You can correct it by using trjconv (once you have assembled a .tpr file): trjconv -s *.tpr -f outfile.pdb -pbc mol -ur compact -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/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] editconf.
Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 I get the error message, Fatal error: Expected a real argument for option -center Can anyone help, Many Thanks, David. -- 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] editconf.
On Dec 21, 2009, at 5:26 PM, david.lisgar...@canterbury.ac.uk david.lisgar...@canterbury.ac.uk wrote: Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 You have to give real coordinates for the center, not in terms of x, y, z. The coordinates are given e.g. at the end of the gro file. Carsten -- 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] editconf.
Carsten Kutzner wrote: On Dec 21, 2009, at 5:26 PM, david.lisgar...@canterbury.ac.uk david.lisgar...@canterbury.ac.uk wrote: Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 You have to give real coordinates for the center, not in terms of x, y, z. The coordinates are given e.g. at the end of the gro file. The dimensions of the box are given at the end of the .gro file. 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] editconf and g_rmsdist
Dear Tsjerk, Thanks for your suggestion. I tried changing the box values, and it still give a deviation, so I have filed a bug report. Best regards, Soren -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent: Friday, September 18, 2009 7:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf and g_rmsdist Hi Soren, Why I am seeing this difference? Is it due to round-off's after the transformation to center the molecule in the box? Or am I using g_rmsdist wrongly? It's a bit weird indeed. You might be right that it's due to round-off errors. You can try to copy the original gro file and replace the last line with4.0 4.0 4.0 to set the box manually. That should rule out whether it's the box, which I can hardly imagine. The other test is to add a shift, but you'd want to make sure that rounding could get an issue then... Hope it helps, 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://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
[gmx-users] editconf and g_rmsdist
Dear GMX-users I have a question about what happens when editconf is used to box a molecule. The reason I ask is because, I have used g_rmsdist in order to study how a very small piece of a structure (100+ atoms) relaxes towards its native state (given by NMR) after a small perturbation. After 10+ ns the distrmsd has not been below 0.25 nm. Tracing back, I realized that the distrmsd was already 0.25 nm after I inserted my NMR structure into the box in the first place! I did the following: 1. editconf -f NMR.gro -o boxed.gro -box 4 4 4 2. /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o distrmsd-boxed-NMR .. Select a group: 0 Selected 0: 'System' .. 3. cat distrmsd-boxed-NMR.xvg # This file was created Fri Sep 18 13:02:06 2009 # by the following command: # /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o distrmsd-boxed-NMR # # /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title RMS Deviation @xaxis label Time (ps) @yaxis label RMSD (nm) @TYPE xy @ subtitle of distances between System atoms 0 0.249025 Just as a test, I tried also *NOT* to box the structure: 1. editconf -f NMR.gro -o test.gro 2. /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o distrmsd-boxed-NMR ... Select a group: 0 Selected 0: 'System' ... 3. cat distrmsd-boxed-NMR.xvg # This file was created Fri Sep 18 13:16:04 2009 # by the following command: # /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o distrmsd-boxed-NMR # # /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title RMS Deviation @xaxis label Time (ps) @yaxis label RMSD (nm) @TYPE xy @ subtitle of distances between System atoms 0 1.83827e-08 Why I am seeing this difference? Is it due to round-off's after the transformation to center the molecule in the box? Or am I using g_rmsdist wrongly? Best regards, Soren ___ 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] editconf and g_rmsdist
Hi Soren, Why I am seeing this difference? Is it due to round-off’s after the transformation to center the molecule in the box? Or am I using g_rmsdist wrongly? It's a bit weird indeed. You might be right that it's due to round-off errors. You can try to copy the original gro file and replace the last line with4.0 4.0 4.0 to set the box manually. That should rule out whether it's the box, which I can hardly imagine. The other test is to add a shift, but you'd want to make sure that rounding could get an issue then... Hope it helps, 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://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] editconf 2 warning
Hi These 2 warning appeared after I did editconf for Drug-Protein Complex. WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Could I ignor these and continue? Thank you for reply. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf 2 warning
Homa Azizian wrote: Hi These 2 warning appeared after I did editconf for Drug-Protein Complex. WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Could I ignor these and continue? We can't tell, since we don't know what your residue and atom names are. You should look at these and compare with the entries in your force field's .atp 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf and genbox using method
Hi, I want to obtain a dodecahedron box to start a simulation of a small peptide. But, even if I use dodecahedron option or octahedron, I obtain a rectangular box. Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows) Command line that I used: pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p editconf -f pep1 -o -bt octahedron -d 0.3 -c genbox -cp out -cs -p pep1 -o pep1_em And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular. Please, somebody help me with this problem. PS. I'm a new user of Gromacs but I'm read all the messages from the www.mail-archive.com/gmx-us...@*gromacs*.orghttp://www.mail-archive.com/gmx-users@gromacs.org about this problem but I still don't understand what I need to do to obtain the correct box. Thank you very much in advance for any suggestion. Marian ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
- Original Message - From: Marian Butu marian.b...@gmail.com Date: Monday, March 9, 2009 21:24 Subject: [gmx-users] editconf and genbox using method To: gmx-users@gromacs.org editconf -f pep1 -o -bt octahedron -d 0.3 -c This command line should provoke some warnings at least. Have a look at them, and a read of editconf -h. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options Nuno Azoia On Mon, 2009-03-09 at 12:23 +0200, Marian Butu wrote: Hi, I want to obtain a dodecahedron box to start a simulation of a small peptide. But, even if I use dodecahedron option or octahedron, I obtain a rectangular box. Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows) Command line that I used: pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p editconf -f pep1 -o -bt octahedron -d 0.3 -c genbox -cp out -cs -p pep1 -o pep1_em And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular. Please, somebody help me with this problem. PS. I'm a new user of Gromacs but I'm read all the messages from the www.mail-archive.com/gmx-users@gromacs.org about this problem but I still don't understand what I need to do to obtain the correct box. Thank you very much in advance for any suggestion. Marian ___ 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 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
- Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Exactly. In my simulations with octahedron box I encounter the same problem. I just transform it in pdb to use it with pymol, that's all. But I have to use the same kind of options Justin use. Nuno Azoia On Mon, 2009-03-09 at 07:10 -0400, Justin A. Lemkul wrote: Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Nuno Gonçalo Azoia Lopes Finishing Research Laboratory Textile Engineering Department Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and genbox using method
Thank you very much. Trjconv works fine. Marian On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Mark Abraham wrote: - Original Message - From: Nuno Azoia naz...@det.uminho.pt Date: Monday, March 9, 2009 21:52 Subject: Re: [gmx-users] editconf and genbox using method To: Discussion list for GROMACS users gmx-users@gromacs.org Hello! Your box isn't rectangular. Your problem is just VMD display the gro file with a rectangular shape. If you need to see your system properly try to transform your .gro file in a .pdb file first, using trjconv. Try trjconv -h to see the options I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file. Actually, I've found trjconv to be necessary. VMD indeed shows a rectangular box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact. The transformation to .pdb, however, is unnecessary. The .gro file can be processed in the same way. -Justin 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf -density 1000
Hi The flag of editconf -density has the default value 1000 editconf -densityreal1000Density (g/l) of the output box achieved by scaling But, my system is running on D2O not H2O Earlier I did not notice this flag and simply use the command editconf to create a box. So, will my simulation go totally wrong without giving the correct density? Thank you Lin ___ 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] editconf -density 1000
Chih-Ying Lin wrote: Hi The flag of editconf -density has the default value 1000 editconf -densityreal1000Density (g/l) of the output box achieved by scaling But, my system is running on D2O not H2O Earlier I did not notice this flag and simply use the command editconf to create a box. So, will my simulation go totally wrong without giving the correct density? Well, if your D2O parameters are accurate, and you equilibrate sufficiently, you may be able to achieve the proper density for your system. -Justin Thank you Lin ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] editconf/genbox problem in Gromacs 4.0
Hi, This is a known bug in 4.0. It has been fixed for 4.0.1, which will hopefully be released today. Berk Date: Fri, 7 Nov 2008 11:23:14 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0 Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb The output from editconf does not report errors, but I noted that the volume of the box is 0! --- output message--- WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in vdwradii.dat: 28 Entries in dgsolv.dat: 7 Entries in electroneg.dat: 71 Entries in elements.dat: 218 Read 16824 atoms Volume: 0 nm^3, corresponds to roughly 0 electrons - 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro -o my_protein_wat.pdb -p my_protein.top The output from genbox_d reports the following error: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- I have performed the same commands on another machine (Linux) running version 3.3 and I produced with success a nice solvent box. Suggestions? Thanks, Caterina -- Caterina Arcangeli ENEA, Dept. Physics (FIM-CAMO) C.R. Casaccia, SP 026 Via Anguillarese 301 - 00123 Roma ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] editconf/genbox problem in Gromacs 4.0
Many thanks to Bert and Xavier. Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. Yes, it works, but I'm using .pdb instead of .gro format to support chain identifiers since my system is composed by 3 protein chains. So I will wait for the new 4.0.1 release. Caterina ___ 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] editconf/genbox problem in Gromacs 4.0
Hi, For the moment you can use editconf of 3.3 or copy a cryst1 entry (one of the first lines) from another pdb file into you pdb input file, editconf will then write the correct box in the output pdb. Berk Date: Fri, 7 Nov 2008 12:13:55 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0 Many thanks to Bert and Xavier. Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. Yes, it works, but I'm using .pdb instead of .gro format to support chain identifiers since my system is composed by 3 protein chains. So I will wait for the new 4.0.1 release. Caterina ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] editconf/genbox problem in Gromacs 4.0
Right! Thanks again Berk. Caterina 2008/11/7 Berk Hess [EMAIL PROTECTED]: Hi, For the moment you can use editconf of 3.3 or copy a cryst1 entry (one of the first lines) from another pdb file into you pdb input file, editconf will then write the correct box in the output pdb. Berk Date: Fri, 7 Nov 2008 12:13:55 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0 Many thanks to Bert and Xavier. Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. Yes, it works, but I'm using .pdb instead of .gro format to support chain identifiers since my system is composed by 3 protein chains. So I will wait for the new 4.0.1 release. Caterina ___ gmx-users mailing list gmx-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 Express yourself instantly with MSN Messenger! MSN Messenger ___ 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] editconf/genbox problem in Gromacs 4.0
Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb The output from editconf does not report errors, but I noted that the volume of the box is 0! --- output message--- WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in vdwradii.dat: 28 Entries in dgsolv.dat: 7 Entries in electroneg.dat: 71 Entries in elements.dat: 218 Read 16824 atoms Volume: 0 nm^3, corresponds to roughly 0 electrons - 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro -o my_protein_wat.pdb -p my_protein.top The output from genbox_d reports the following error: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- I have performed the same commands on another machine (Linux) running version 3.3 and I produced with success a nice solvent box. Suggestions? Thanks, Caterina -- Caterina Arcangeli ENEA, Dept. Physics (FIM-CAMO) C.R. Casaccia, SP 026 Via Anguillarese 301 - 00123 Roma ___ 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] editconf/genbox problem in Gromacs 4.0
On Fri, 7 Nov 2008 11:23:14 +0100 Caterina Arcangeli [EMAIL PROTECTED] wrote: Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. The output from editconf does not report errors, but I noted that the volume of the box is 0! --- output message--- WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Entries in vdwradii.dat: 28 Entries in dgsolv.dat: 7 Entries in electroneg.dat: 71 Entries in elements.dat: 218 Read 16824 atoms Volume: 0 nm^3, corresponds to roughly 0 electrons - 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro -o my_protein_wat.pdb -p my_protein.top The output from genbox_d reports the following error: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- I have performed the same commands on another machine (Linux) running version 3.3 and I produced with success a nice solvent box. Suggestions? Thanks, Caterina -- Caterina Arcangeli ENEA, Dept. Physics (FIM-CAMO) C.R. Casaccia, SP 026 Via Anguillarese 301 - 00123 Roma ___ 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 - XAvier Periole - PhD - Molecular Dynamics Group - NMR and Computation University of Groningen The Netherlands - ___ 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] editconf/genbox problem in Gromacs 4.0
Users, I have recently upgraded from Gromacs3.3 to Gromacs4.0 and I seem to be encountering a problem when trying to solvate a protein in a water box. Editconf command: editconf -bt octahedron -f prot2.pdb -o prot2_test.pdb -c -d 1.0 The output from editconf appears to be normal and the problem doesn't arise until i issue the genbox command: genbox -cp prot2_test.pdb -cs spc216.gro -o prot_4ion.pdb -p prot.top Error message that follows: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- On another machine running version 3.3 i have issued the same commands and there is no error message. When examining the difference between the prot2_test.pdb files, version 4.0 seems to be leaving out the line containing coordinate information about the water box. Line missing @ the top of the prot2_test.pdb in version 4.0: CRYST1 96.102 96.102 96.102 70.53 109.47 70.53 P 1 1 Has anyone else experienced this problem? Are there any flags that i am missing that i now need to specify? Any information would be appreciated. Thanks, Matt Danielson ___ 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] editconf subroutine
Hello, I how does editconf subroutine calculate the triclinc box dimensions (v1(x), v2(y), v3(z), v1(y) etc) from, for example, a .pdf file that has lattice dimensions information (a, b, c, alpha, beta, gamma). I would really appreciate a mathematical formula for each of these elements (v1(x), v2(y), v3(z), v1(y) etc) or at least where can I find this information? Thank you maria ___ 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] editconf -mead
Dear Marco, Which version? Ran. marcos wrote: Hi, editconf -mead writes a .pqr with a format %10.5f%10.5f%10.5f while it should be %8.3f%8.3f%8.3f. Also the charges and radius are written in %8.4f%8.4f while the program pdb2pqr writes as %8.4f%7.4f I changed line 167 of pdbio.c from: strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n); to strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n); and the .pqr is now ok. Will this change affect other programs? Thanks, Marcos Villarreal ___ 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] editconf -mead
Hi, editconf -mead writes a .pqr with a format %10.5f%10.5f%10.5f while it should be %8.3f%8.3f%8.3f. Also the charges and radius are written in %8.4f%8.4f while the program pdb2pqr writes as %8.4f%7.4f I changed line 167 of pdbio.c from: strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n); to strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n); and the .pqr is now ok. Will this change affect other programs? Thanks, Marcos Villarreal ___ 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] editconf -mead
3.3.1 and 3.3.2 IIRC in 3.1.4 it was ok Marcos On Wed, 2007-10-31 at 18:34 +0100, Ran Friedman wrote: Dear Marco, Which version? Ran. marcos wrote: Hi, editconf -mead writes a .pqr with a format %10.5f%10.5f%10.5f while it should be %8.3f%8.3f%8.3f. Also the charges and radius are written in %8.4f%8.4f while the program pdb2pqr writes as %8.4f%7.4f I changed line 167 of pdbio.c from: strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n); to strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n); and the .pqr is now ok. Will this change affect other programs? Thanks, Marcos Villarreal ___ 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] editconf -mead
marcos wrote: Hi, editconf -mead writes a .pqr with a format %10.5f%10.5f%10.5f while it should be %8.3f%8.3f%8.3f. Also the charges and radius are written in %8.4f%8.4f while the program pdb2pqr writes as %8.4f%7.4f I changed line 167 of pdbio.c from: strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n); to strcpy(pdbform,%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n); and the .pqr is now ok. Will this change affect other programs? I'm not aware that there is a standard for the PQR format. It's a hacked derivative of a PDB file. Some software that claims to read them probably constrains the format as for a PDB file, but others expect a free-form white-space-delimited format (e.g APBS, for which pdb2pqr prepares input). The two are not mutually consistent, so there will be problems. It's straightforward to write a Perl script to convert from the above formats you describe in order to make some PQR-reading software happy. If someone writes one, add it to the contributions section of the GROMACS webpage. 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] editconf and the placement of the center of mass
Hi Arneh, From the help of editconf (editconf -h) you could have seen that it has no such option. It wouldn't be very hard to add it though... Cheers, Tsjerk On 8/8/07, Arneh Babakhani [EMAIL PROTECTED] wrote: Hi, In editconf, there's an option -center which allows you to place the geometrical center of your molecular at a desired location. I was wondering, is there an analogous option for the placement of the center of mass of a molecule? Thanks, Arneh ___ 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 -- 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
[gmx-users] editconf and the placement of the center of mass
Hi, In editconf, there's an option -center which allows you to place the geometrical center of your molecular at a desired location. I was wondering, is there an analogous option for the placement of the center of mass of a molecule? Thanks, Arneh ___ 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] editconf -translate help
Shayla Fitzsimmons wrote: I have a box which contains a slab of carbon (solid) that is centered within the box. However, I want the slab to be at the very right side of the box - I know I must use editconf -translate to do this, however I cannot seem to make it work. The slab is centered has the same height and width (y and z coordinates) of the box, however it is one third of the length (the x coordinate). Graphically, at the moment, it looks like this: _ | xxx | | xxx | |___xxx___| Where 'xx' is my slab (that is how the view comes up when I open the file in rasmol). The dimensions of the box (as listed in the .gro file) are 13.90030 4.02160 5.36640 As I previously said, I want the slab to be on the right side of the box, not the center, however I have tried several different things and it does not seem to want to work for me (however, I am unsure if I am using the proper values for -translate). What X Y Z coordinates should I use for this to translate it? the difference between new and old com. most likely 5 0 0 will do the trick. Thanks! S F ___ 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 -- 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
[gmx-users] editconf (protein+bilayer)
Dear all I have a pdb of my protein. I want to position of protein in x,y and z relative to the bilayer .how can i do by editconf? rhanks Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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] editconf (protein+bilayer)
mahbubeh zarrabi wrote: Dear all I have a pdb of my protein. I want to position of protein in x,y and z relative to the bilayer .how can i do by editconf? rhanks editconf -h (always a good start) editconf -translate -n Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ 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 -- 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] editconf
Why not copy the coordinates of the channel in to th lipid's file? Itamr. mahbubeh zarrabi wrote: Dear gmx_users I am trying to insert one channel peptide in lipid bilayer. I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University, Givat-Ram | Jerusalem, 91904, Israel | Tel: +972-(0)2-6585194 | Fax: +972-(0)2-6584329 | Email: [EMAIL PROTECTED] | Net: http://membranelab.huji.ac.il/itamar_homepage/itamar_homepage.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] editconf
editconf -h editconf -translate ... cat xxx.pdb yyy.pdb and remove the TER and ENDMDL lines Good luck, Jochen mahbubeh zarrabi wrote: Dear gmx_users I am trying to insert one alpha-helical peptide . I created two pdbs, bilayer.pdb and peptide.pdb . how can i were adjusted the peptide coordinates using editconf to be at the desired vertical position in the bilayer. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] editconf -d
==Original message text===On Wed, 19 Jul 2006 10:18:30 EDT Isabella Daidone wrote:-d is not for centering. -d is the distance of the protein from the walls of the box.Hi,when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box.In gromacs version 3.3, does option -d in editconf really imply that the protein will be centered or is there still a bug (as in version 3.2.1) or am I missing something?ThanksIsabella___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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===End of original message text! === ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] editconf
Beniamino Sciacca wrote: Hi! I've another question: I've a DNA molecule, and I make a rigid traslation of the entire system. If I try to display the new molecule with VMD, it doesn't display anything! Instead if I run editconf on the new traslated molecule VMD works and I see the molecule, but using editconf the position of the molecule changes. Why? My guess is you are translating the molecule in the direction of the VMD viewer and it is behind the projection point, and that a subsequent editconf is re-centering it. Use the VMD tools for changing the viewpoint, and/or showing the axes to test. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
