[gmx-users] converting all-atom pdb to cg.pdb
Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, C, etc) in the pdb file of a multimeric protein? From ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00 C ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00 C ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00 C ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00 C ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00 C ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00 O ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00 N I get ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00 ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00 ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00 i.e., weird residue numbers. In another case (coming from AMBER, where the subunit indication is omitted) with the subunit indicated, the residue numbers in the cg file are correct. I don't see any other difference between the two starting files. Or should I look for a different cause. thanks francesco pietra ... -- 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] converting all-atom pdb to cg.pdb
Francesco Pietra wrote: Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, C, etc) in the pdb file of a multimeric protein? From ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00 C ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00 C ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00 C ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00 C ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00 C ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00 O ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00 N I get ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00 ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00 ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00 i.e., weird residue numbers. The awk script simply copies the information from one line to the new file, using the old atom numbers. You can use genconf -renumber to fix this. The reason why the residue number isn't being written is because there is a problem with the atom2cg script that I have posted here a number of times. For example, you need to fix each line of the script: OLD LINE if($1==ATOM $4==ARG $3==CA) printf(%4s %5i %4s %3s %4s%8.3f%8.3f%8.3f%6.2f%6.2f\n,$1, $2, BN0, $4, $6, $7, $8, $9,$10,$11); FIXED LINE if($1==ATOM $4==ARG $3==CA) printf(%4s %5i %4s %3s %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n,$1, $2, BN0, $4, $5, $6, $7, $8, $9,$10,$11); In another case (coming from AMBER, where the subunit indication is omitted) with the subunit indicated, the residue numbers in the cg file are correct. I don't see any other difference between the two starting files. Or should I look for a different cause. Then that's simply a matter of luck :) The print statements in the original awk script do not expect chain identifiers, so the printing worked due to the extra field. -Justin thanks francesco pietra ... -- Justin A. Lemkul Ph.D. Candidate 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://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] Problem with topolbuild
On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: I have a small organic molecule that I processed with antechamber using the gaff forcefield and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried to use the program topolbuild version 1.2 from the GROMACS website. when I execute the command: topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40 I get this error message: Fatal error. Source code file: readmol2.c, line: 109 Atomic symbol cc in atom type not found. When I excecute the topolbuild above I use -dir ../ because that should take the program to the directory containing dat/antechamber and etc. which actually comes with the topolbuild 1.2 package I don't know what to do and I have tried searching this mailing list and google without sucess. Can someone please help me? First, the mol2 file that you are using is not syntactically correct because it is using gaff atom types and not Tripos' Sybyl atom types. A syntactically correct mol2 file would not have atom type cc. Please process your organic molecule against the Sybyl force field to get a correct mol2 file. Second, there are a number of bug fixes I have placed in this list for version 1.2.1 which is the version I hope you are using. The following diffs should be applied: diff topolbuild1_2_1/src/Makefile topolbuild1_2_2/src/Makefile 22,23c22,29 $(PROGRAM): $(SOURCES) $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- $(PROGRAM): $(OBJECTS) $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm clean: rm -f *.o dist_clean: rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/Makefile.G4OsX topolbuild1_2_2/src/Makefile.G4OsX 22,23c22,29 $(PROGRAM): $(SOURCES) $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- $(PROGRAM): $(OBJECTS) $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm clean: rm -f *.o dist_clean: rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/ring_detect.c topolbuild1_2_2/src/ring_detect.c 450c450 ar_set[(t_ring_atomno[i][j])][3]++; --- ar_set[(t_ring_atomno[i][k])][3]++; diff topolbuild1_2_1/src/topolbuild.c topolbuild1_2_2/src/topolbuild.c 440c440 max_rng = num_bonds/2; --- max_rng = 3 * num_bonds/4; Also, when using Gromacs force fields, the defaults definition line needs to be changed from: 1 2 yes 0.5 0.8333 to: 1 1 no 1.0 1.0 Unfortunately, I did not allow for different defaults for different force fields in that version. The next version will correct that as well as adding OPLSAA to the suite of force fields available. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] Can not find forcefield for atom C4-1 with 0 bonds
Darrell Koskinen wrote: Hi, I am trying to create a topology file from a .gro file. When I run x2top with methane (C4 opls_066) in my .gro file, I receive the following warning: /Can not find forcefield for atom C4-1 with 0 bonds/ I have included the following line in the ffoplsaa.n2t file, which resides in my working directory: /C4 opls_0660 16.043 0/ I thought that the inclusion of the name to type definition for C4 in the .n2t file would have resolved the above warning. Please let me know if there is something else I must do to resolve this problem. It appears that x2top simply does not work if there aren't any bonds. I suppose that makes sense; the topology for a united-atom methane would be a single [ atoms ] entry, which is trivial to create by hand. -Justin Thanks. Darrell -- Justin A. Lemkul Ph.D. Candidate 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://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] Problem with topolbuild
Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? Thanks On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: I have a small organic molecule that I processed with antechamber using the gaff forcefield and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried to use the program topolbuild version 1.2 from the GROMACS website. when I execute the command: topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40 I get this error message: Fatal error. Source code file: readmol2.c, line: 109 Atomic symbol cc in atom type not found. When I excecute the topolbuild above I use -dir ../ because that should take the program to the directory containing dat/antechamber and etc. which actually comes with the topolbuild 1.2 package I don't know what to do and I have tried searching this mailing list and google without sucess. Can someone please help me? First, the mol2 file that you are using is not syntactically correct because it is using gaff atom types and not Tripos' Sybyl atom types. A syntactically correct mol2 file would not have atom type cc. Please process your organic molecule against the Sybyl force field to get a correct mol2 file. Second, there are a number of bug fixes I have placed in this list for version 1.2.1 which is the version I hope you are using. The following diffs should be applied: diff topolbuild1_2_1/src/Makefile topolbuild1_2_2/src/Makefile 22,23c22,29 $(PROGRAM): $(SOURCES) $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- $(PROGRAM): $(OBJECTS) $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm clean: rm -f *.o dist_clean: rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/Makefile.G4OsX topolbuild1_2_2/src/Makefile.G4OsX 22,23c22,29 $(PROGRAM): $(SOURCES) $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- $(PROGRAM): $(OBJECTS) $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm clean: rm -f *.o dist_clean: rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/ring_detect.c topolbuild1_2_2/src/ring_detect.c 450c450 ar_set[(t_ring_atomno[i][j])][3]++; --- ar_set[(t_ring_atomno[i][k])][3]++; diff topolbuild1_2_1/src/topolbuild.c topolbuild1_2_2/src/topolbuild.c 440c440 max_rng = num_bonds/2; --- max_rng = 3 * num_bonds/4; Also, when using Gromacs force fields, the defaults definition line needs to be changed from: 1 2 yes 0.5 0.8333 to: 1 1 no 1.0 1.0 Unfortunately, I did not allow for different defaults for different force fields in that version. The next version will correct that as well as adding OPLSAA to the suite of force fields available. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] g_energy
Thanks allot for the ultrafast response and above all your help !. Arik Mark Abraham wrote: Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a flag that I can give the program and thus skip the part when the g_energy program asks for an input for the Potential/Temperature... option(much like -ff for the force field in the runmd program) See http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive Mark No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.425 / Virus Database: 270.14.57/2492 - Release Date: 11/09/09 12:11:00 -- 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] Problem with topolbuild
On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? For short patches like these, I just use a text editor. Because the mailing list does not like the length this would come to if I were to attach the edited files, I've sent a separate e-mail to you directly with the edited files for you to place in the topolbuild source directory and recompile. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] Free energy calculations
I'm interesting to calculate Gibbs energy using g_lie application. Unfourtunately, I don't know what kind of state equation is the sub-program using. Can you help me with that. Best regards Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Experimental Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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] S-type Hydrogen bond correlation function
I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? Now if i install will i get the trajectory? Is API available for gromacs? Thank you. write_trx(out,natoms,swi,top.atoms,0,t,box,x,NULL); } /* } while(read_next_x(status,t,natoms,x,box)); */ } while(read_next_frame(status,fr)); close_trj(status); if (out != -1) close_trx(out); if (fp) ffclose(fp); thanx(stderr); return 0; } On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. It seems likely to be straightforward to change the main loop of gmx_trjorder to use read_next_frame, which will permit it to read and write velocities and forces if they are present. I don't have time to do it, though. Mark On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: She's a Good Sheila Bruce (Monty Python) --- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6,
[gmx-users] MD with bilayer
Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. the initial step - pdb2gmx is not working for this complex(pdb+membrane) thanks in advance Parthiban -- 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] Problem with topolbuild
It works. Thank you so much. Regards, Gunnar W. On Mon, Nov 9, 2009 at 4:26 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? For short patches like these, I just use a text editor. Because the mailing list does not like the length this would come to if I were to attach the edited files, I've sent a separate e-mail to you directly with the edited files for you to place in the topolbuild source directory and recompile. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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] MD with bilayer
Hi, VMD was built to work with NAMD, so the atom names and topologies will not work with GROMACS. I guess you better go to Peter Tieleman site ( http://moose.bio.ucalgary.ca/) and rad there how to do things. Cheers, Itamar On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham mark.abra...@anu.edu.auwrote: parthi...@ncbs.res.in wrote: Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. Follow the methods of whichever tutorial you learned from :-) the initial step - pdb2gmx is not working for this complex(pdb+membrane) We're not omniscient... tell us what you did, what you expected, what you saw and why you think it was not working :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users 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] MD with bilayer
parthi...@ncbs.res.in wrote: Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. Follow the methods of whichever tutorial you learned from :-) the initial step - pdb2gmx is not working for this complex(pdb+membrane) We're not omniscient... tell us what you did, what you expected, what you saw and why you think it was not working :-) 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] S-type Hydrogen bond correlation function
Ramachandran G wrote: I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? You could try it, but it won't work. The whole do...while loop needs to be adjusted to use fr and its struct members, rather than separate box, t, x, etc. Also read_first_frame is required before the loop, not whatever is used there. Now if i install will i get the trajectory? Is API available for gromacs? Thank you. Pre 4.1, API documentation is patchy at best. You can see how this machinery gets used by comparing with the source code of a tool that read and write non-position data, e.g. gmxdump and doubtless others. Obviously, you'll need to recompile and re-install to use any new version. Mark write_trx(out,natoms,swi,top.atoms,0,t,box,x,NULL); } /* } while(read_next_x(status,t,natoms,x,box)); */ } while(read_next_frame(status,fr)); close_trj(status); if (out != -1) close_trx(out); if (fp) ffclose(fp); thanx(stderr); return 0; } On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. It seems likely to be straightforward to change the main loop of gmx_trjorder to use read_next_frame, which will permit it to read and write velocities and forces if they are present. I don't have time to do it, though. Mark On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing. So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. First, your .mdp must specify the recording of velocities. Then consult the documentation for trjorder and g_velacc for what you want. Mark On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. - Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 3 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540-666.000 One-way 0.074 13.435 10.968 Integral0.047 21.471 12.130 Relaxation 0.047
[gmx-users] Missing H from residue
I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Missing H from residue
Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. This is the residue in question ATOM 1 N GLU32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 GLU32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 GLU32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA GLU32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 GLU32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 GLU32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 GLU32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 GLU32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 GLU32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 GLU32 -20.892 8.644 -5.172 1.00 0.00 H [boinc...@vps test]$ grep -A5 GLU /usr/local/gromacs/share/gromacs/top/ffamber99sb.* /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb:GLU4 /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 1 H N -C CA /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 5 HA CA N CB C /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HB CB CA CG /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HG CG CB CD /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-ASP3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad:[ GLU ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- [ atoms ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- N amber99sb_34 -0.51630 1 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- H amber99sb_17 0.29360 2 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-CA amber99sb_11 0.03970 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-HA amber99sb_19 0.11050 4 On Mon, Nov 9, 2009 at 4:26 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? Yep - you may need a well-formatted .hdb file, like the message says :-) You should check out whether the AMBER port you installed supports this feature or not. Alternatively, have a look in the file and with a viewer to see what is present for residue 1 and how the atoms are named, and whether renaming some atoms will fix the issue. Mark WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- 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/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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Missing H from residue
Jack Shultz wrote: I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) When using AMBER, the first residue should be NGLU, not just GLU. Likewise for the C-terminus (CXXX). If you name the residue appropriately, the right hydrogens should be added based on the .hdb entry. -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- Justin A. Lemkul Ph.D. Candidate 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://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] Missing H from residue
Jack Shultz wrote: Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. Non-standard? H[ABGDEZ][123] are the H atoms for the heavy atom that is alpha through zeta to the backbone carbonyl. This is the residue in question ATOM 1 N GLU32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 GLU32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 GLU32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA GLU32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 GLU32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 GLU32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 GLU32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 GLU32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 GLU32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 GLU32 -20.892 8.644 -5.172 1.00 0.00 H [boinc...@vps test]$ grep -A5 GLU /usr/local/gromacs/share/gromacs/top/ffamber99sb.* /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb:GLU4 /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 1 H N -C CA So here, for GLU, the H can't be constructed because there is no C from a preceding residue. Hence the need for NGLU per Justin's suggestion. However your grep should have found NGLU if you have a complete installation. Mark /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1 5 HA CA N CB C /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HB CB CA CG /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2 6 HG CG CB CD /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-ASP3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad:[ GLU ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- [ atoms ] /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- N amber99sb_34 -0.51630 1 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- H amber99sb_17 0.29360 2 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-CA amber99sb_11 0.03970 3 /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-HA amber99sb_19 0.11050 4 On Mon, Nov 9, 2009 at 4:26 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there an easy way to add missing atoms? Yep - you may need a well-formatted .hdb file, like the message says :-) You should check out whether the AMBER port you installed supports this feature or not. Alternatively, have a look in the file and with a viewer to see what is present for residue 1 and how the atoms are named, and whether renaming some atoms will fix the issue. Mark WARNING: atom H is missing in residue GLU 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLU in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing --- -- 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
Re: [gmx-users] Free energy calculations
Can you be more specific in the question of what property you want to compute for which molecule or molecules? Linear Interaction energy approaches are not always very efficient for coulomb, and is definitely not exact for the LJ term. So LIE might not be what you want to be doing. Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 On Mon, Nov 9, 2009 at 1:49 PM, jorge_quint...@ciencias.uis.edu.co wrote: I'm interesting to calculate Gibbs energy using g_lie application. Unfourtunately, I don't know what kind of state equation is the sub-program using. Can you help me with that. Best regards Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Experimental Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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/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] Missing H from residue
I modified the N-Terminal and C-Terminal Residues. [boinc...@vps test]$ grep NGLU ProteinAmber.pdb grep CARG ProteinAmber.pdb ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C NGLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O NGLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB NGLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG NGLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD NGLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 NGLU 32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 NGLU 32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA NGLU 32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 NGLU 32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 NGLU 32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 NGLU 32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 NGLU 32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 NGLU 32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 NGLU 32 -20.892 8.644 -5.172 1.00 0.00 H ATOM 3819 N CARG 153 -2.889 -18.736 0.849 1.00 0.00 N ATOM 3820 CA CARG 153 -4.210 -19.301 1.173 1.00 0.00 C ATOM 3821 C CARG 153 -4.155 -20.743 1.653 1.00 0.00 C ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O ATOM 3823 CB CARG 153 -5.123 -19.172 -0.074 1.00 0.00 C ATOM 3824 CG CARG 153 -5.347 -17.677 -0.414 1.00 0.00 C ATOM 3825 CD CARG 153 -6.074 -17.485 -1.764 1.00 0.00 C ATOM 3826 NE CARG 153 -7.488 -17.868 -1.625 1.00 0.00 N ATOM 3827 CZ CARG 153 -8.038 -19.003 -1.986 1.00 0.00 C ATOM 3828 NH1 CARG 153 -7.368 -20.017 -2.446 1.00 0.00 N ATOM 3829 NH2 CARG 153 -9.327 -19.146 -1.882 1.00 0.00 N ATOM 3830 HA CARG 153 -4.670 -18.715 1.987 1.00 0.00 H ATOM 3831 OXT CARG 153 -3.778 -21.646 0.751 1.00 0.00 O ATOM 3832 HT CARG 153 -3.770 -22.506 1.154 1.00 0.00 H ATOM 3833 HB1 CARG 153 -4.628 -19.690 -0.911 1.00 0.00 H ATOM 3834 HB2 CARG 153 -6.096 -19.657 0.114 1.00 0.00 H ATOM 3835 HG1 CARG 153 -5.942 -17.224 0.393 1.00 0.00 H ATOM 3836 HG2 CARG 153 -4.393 -17.125 -0.460 1.00 0.00 H ATOM 3837 HD1 CARG 153 -6.049 -16.397 -1.960 1.00 0.00 H ATOM 3838 HD2 CARG 153 -5.519 -17.914 -2.612 1.00 0.00 H ATOM 3839 HE CARG 153 -8.133 -17.122 -1.290 1.00 0.00 H ATOM 3840 1HH1 CARG 153 -7.834 -20.881 -2.736 1.00 0.00 H ATOM 3841 2HH1 CARG 153 -6.359 -19.962 -2.559 1.00 0.00 H ATOM 3842 1HH2 CARG 153 -9.802 -20.000 -2.173 1.00 0.00 H ATOM 3843 2HH2 CARG 153 -9.904 -18.331 -1.627 1.00 0.00 H ATOM 3844 HN CARG 153 -2.612 -18.555 -0.097 1.00 0.00 H TER3845 CARG 153 This time I did not protonate with babel pdb2gmx -ff amber99sb -f ProteinAmber.pdb -ignh Back Off! I just backed up topol.top to ./#topol.top.6# Processing chain 1 (1976 atoms, 244 residues) There are 362 donors and 364 acceptors There are 561 hydrogen bonds --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O On Mon, Nov 9, 2009 at 6:54 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. Non-standard? H[ABGDEZ][123] are the H atoms for the heavy atom that is alpha through zeta to the backbone carbonyl. This is the residue in question ATOM 1 N GLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C GLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O GLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB GLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG GLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD GLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM
Re: [gmx-users] Missing H from residue
Jack Shultz wrote: I modified the N-Terminal and C-Terminal Residues. [boinc...@vps test]$ grep NGLU ProteinAmber.pdb grep CARG ProteinAmber.pdb ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C NGLU 32 -20.807 7.451 -2.751 1.00 0.00 C ATOM 4 O NGLU 32 -21.843 7.183 -3.340 1.00 0.00 O ATOM 5 CB NGLU 32 -19.913 9.782 -2.416 1.00 0.00 C ATOM 6 CG NGLU 32 -18.641 10.678 -2.498 1.00 0.00 C ATOM 7 CD NGLU 32 -18.573 11.627 -1.334 1.00 0.00 C ATOM 8 OE1 NGLU 32 -19.009 12.797 -1.488 1.00 0.00 O ATOM 9 OE2 NGLU 32 -18.089 11.174 -0.257 1.00 0.00 O ATOM 10 HA NGLU 32 -18.845 8.057 -3.227 1.00 0.00 H ATOM 11 HB1 NGLU 32 -20.805 10.368 -2.695 1.00 0.00 H ATOM 12 HB2 NGLU 32 -20.026 9.493 -1.358 1.00 0.00 H ATOM 13 HG1 NGLU 32 -17.724 10.072 -2.453 1.00 0.00 H ATOM 14 HG2 NGLU 32 -18.628 11.255 -3.435 1.00 0.00 H ATOM 15 HT2 NGLU 32 -19.381 9.526 -5.140 1.00 0.00 H ATOM 16 HT1 NGLU 32 -20.892 8.644 -5.172 1.00 0.00 H ATOM 3819 N CARG 153 -2.889 -18.736 0.849 1.00 0.00 N ATOM 3820 CA CARG 153 -4.210 -19.301 1.173 1.00 0.00 C ATOM 3821 C CARG 153 -4.155 -20.743 1.653 1.00 0.00 C ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O ATOM 3823 CB CARG 153 -5.123 -19.172 -0.074 1.00 0.00 C ATOM 3824 CG CARG 153 -5.347 -17.677 -0.414 1.00 0.00 C ATOM 3825 CD CARG 153 -6.074 -17.485 -1.764 1.00 0.00 C ATOM 3826 NE CARG 153 -7.488 -17.868 -1.625 1.00 0.00 N ATOM 3827 CZ CARG 153 -8.038 -19.003 -1.986 1.00 0.00 C ATOM 3828 NH1 CARG 153 -7.368 -20.017 -2.446 1.00 0.00 N ATOM 3829 NH2 CARG 153 -9.327 -19.146 -1.882 1.00 0.00 N ATOM 3830 HA CARG 153 -4.670 -18.715 1.987 1.00 0.00 H ATOM 3831 OXT CARG 153 -3.778 -21.646 0.751 1.00 0.00 O ATOM 3832 HT CARG 153 -3.770 -22.506 1.154 1.00 0.00 H ATOM 3833 HB1 CARG 153 -4.628 -19.690 -0.911 1.00 0.00 H ATOM 3834 HB2 CARG 153 -6.096 -19.657 0.114 1.00 0.00 H ATOM 3835 HG1 CARG 153 -5.942 -17.224 0.393 1.00 0.00 H ATOM 3836 HG2 CARG 153 -4.393 -17.125 -0.460 1.00 0.00 H ATOM 3837 HD1 CARG 153 -6.049 -16.397 -1.960 1.00 0.00 H ATOM 3838 HD2 CARG 153 -5.519 -17.914 -2.612 1.00 0.00 H ATOM 3839 HE CARG 153 -8.133 -17.122 -1.290 1.00 0.00 H ATOM 3840 1HH1 CARG 153 -7.834 -20.881 -2.736 1.00 0.00 H ATOM 3841 2HH1 CARG 153 -6.359 -19.962 -2.559 1.00 0.00 H ATOM 3842 1HH2 CARG 153 -9.802 -20.000 -2.173 1.00 0.00 H ATOM 3843 2HH2 CARG 153 -9.904 -18.331 -1.627 1.00 0.00 H ATOM 3844 HN CARG 153 -2.612 -18.555 -0.097 1.00 0.00 H TER3845 CARG 153 This time I did not protonate with babel pdb2gmx -ff amber99sb -f ProteinAmber.pdb -ignh Back Off! I just backed up topol.top to ./#topol.top.6# Processing chain 1 (1976 atoms, 244 residues) There are 362 donors and 364 acceptors There are 561 hydrogen bonds --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O Yes, but the residue number doesn't make sense. Since you have 153+1 - 32 = 122 residues and pdb2gmx doesn't like number 244, I guess that you have two structures in your .pdb file. If so, I posted some coping strategies in the last week or two for this case. Telling us what (you think) is in your structure file would have been a good idea :-) Mark On Mon, Nov 9, 2009 at 6:54 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. Non-standard? H[ABGDEZ][123] are the H atoms for the heavy atom that is alpha through zeta to the backbone carbonyl. This is the residue in question ATOM 1 N GLU32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA GLU32 -19.847 8.507 -3.304 1.00 0.00 C ATOM
Re: [gmx-users] Missing H from residue
Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG - you should have an O1 and O2 atom for the C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate 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://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] Missing H from residue
On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG [ CARG ] [ atoms ] Namber99_34 -0.34810 1 Hamber99_17 0.27640 2 CAamber99_11 -0.30680 3 HAamber99_19 0.14470 4 CBamber99_11 -0.03740 5 HB1amber99_18 0.03710 6 HB2amber99_18 0.03710 7 CGamber99_11 0.07440 8 HG1amber99_18 0.01850 9 HG2amber99_18 0.0185010 CDamber99_11 0.1114011 HD1amber99_19 0.0468012 HD2amber99_19 0.0468013 NEamber99_38 -0.5564014 HEamber99_17 0.3479015 CZamber99_30.8368016 NH1amber99_38 -0.8737017 HH11amber99_17 0.4493018 HH12amber99_17 0.4493019 NH2amber99_38 -0.8737020 HH21amber99_17 0.4493021 HH22amber99_17 0.4493022 Camber99_20.8557023 OC1amber99_45 -0.8266024 OC2amber99_45 -0.8266025 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms --- C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate 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 list gmx-us...@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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Missing H from residue
Jack Shultz wrote: On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG [ CARG ] [ atoms ] Namber99_34 -0.34810 1 Hamber99_17 0.27640 2 CAamber99_11 -0.30680 3 HAamber99_19 0.14470 4 CBamber99_11 -0.03740 5 HB1amber99_18 0.03710 6 HB2amber99_18 0.03710 7 CGamber99_11 0.07440 8 HG1amber99_18 0.01850 9 HG2amber99_18 0.0185010 CDamber99_11 0.1114011 HD1amber99_19 0.0468012 HD2amber99_19 0.0468013 NEamber99_38 -0.5564014 HEamber99_17 0.3479015 CZamber99_30.8368016 NH1amber99_38 -0.8737017 HH11amber99_17 0.4493018 HH12amber99_17 0.4493019 NH2amber99_38 -0.8737020 HH21amber99_17 0.4493021 HH22amber99_17 0.4493022 Camber99_20.8557023 OC1amber99_45 -0.8266024 OC2amber99_45 -0.8266025 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O Forgive my typo, what I meant was OC1 and OC2. You must always make sure the atoms in the structure file match those expected by the .rtp file. You need OC1 and OC2. -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms --- C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate 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://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 -- Justin A. Lemkul Ph.D. Candidate 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://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] Missing H from residue
Thanks Justin! Got it now. On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms --- But we got an O here ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O The error is not telling you that the O atom is missing from the .pdb file; it is telling you that it is present in the .pdb, but not in the .rtp entry. Look at the .rtp entry for CARG [ CARG ] [ atoms ] N amber99_34 -0.34810 1 H amber99_17 0.27640 2 CA amber99_11 -0.30680 3 HA amber99_19 0.14470 4 CB amber99_11 -0.03740 5 HB1 amber99_18 0.03710 6 HB2 amber99_18 0.03710 7 CG amber99_11 0.07440 8 HG1 amber99_18 0.01850 9 HG2 amber99_18 0.01850 10 CD amber99_11 0.11140 11 HD1 amber99_19 0.04680 12 HD2 amber99_19 0.04680 13 NE amber99_38 -0.55640 14 HE amber99_17 0.34790 15 CZ amber99_3 0.83680 16 NH1 amber99_38 -0.87370 17 HH11 amber99_17 0.44930 18 HH12 amber99_17 0.44930 19 NH2 amber99_38 -0.87370 20 HH21 amber99_17 0.44930 21 HH22 amber99_17 0.44930 22 C amber99_2 0.85570 23 OC1 amber99_45 -0.82660 24 OC2 amber99_45 -0.82660 25 - you should have an O1 and O2 atom for the I made the following modification ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O Forgive my typo, what I meant was OC1 and OC2. You must always make sure the atoms in the structure file match those expected by the .rtp file. You need OC1 and OC2. -Justin --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 122 not found in rtp entry with 25 atoms while sorting atoms --- C-terminal carboxylate. -Justin -- Justin A. Lemkul Ph.D. Candidate 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 list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate 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 list gmx-us...@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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Please tell me how to simulate two structures together in a water box
Respected Sir, Please tell me how to simulate two different stuctures together in a water box so as to have an idea of drug docking and what options to use. Any suggestions are welcome. With Regards Radhika Connect more, do more and share more with Yahoo! India Mail. Learn more. http://in.overview.mail.yahoo.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/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] (no subject)
After installing gromacs4.0 on windows it created Gromacs directory containing several .exe files in bin directory. But when I used pdb2gmx command it will shows that basch command is not found. So anyone can tell me what is that. -- Pawan Kumar Raghav Bioinformatician Stem Cell and Gene Therapy Research Group INMAS, DRDO Timarpur Delhi-110054 -- 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] (no subject)
pawan raghav wrote: After installing gromacs4.0 on windows it created Gromacs directory containing several .exe files in bin directory. But when I used pdb2gmx command it will shows that basch command is not found. So anyone can tell me what is that. See point 8 here http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions 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] Please tell me how to simulate two structures together in a water box
radhika jaswal wrote: Respected Sir, Please tell me how to simulate two different stuctures together in a water box so as to have an idea of drug docking and what options to use. Any suggestions are welcome. Your question is too general. If you need help with GROMACS workflows, you should explore some tutorial material. If you need to design your method, you should start with reading literature. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology file in .dat format
Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.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/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] topology file in .dat format
Hi Subarna, There is no .dat format for topologies. It may be named .dat, but the inside (format) is what matters. If you're confident it is gromos96 format, you can #include it the same way as other molecule definition topology files. Do mind that there's quite a difference between GROMOS96 43a1, 43a2, 45a3, 53a5 and 53a6... Cheers, Tsjerk On Tue, Nov 10, 2009 at 8:30 AM, subarna thakur thakur.suba...@yahoo.co.in wrote: Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. -- 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/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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
