[gmx-users] The problem of .trr file size limit?
Hello, everyone I submit a job with gromacs-4.5.4 in cluster ,but the md.trr file can not write if the file size more than 17247,252,480K(about 16.06G)? and the program always output :Cannot write trajectory frame; maybe you are out of quota? There is sufficient disk space,and the system is redhat 64. Could you give me some solutions? Thanks! -- 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] %hbond number problem
Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and the output info is nothing? So, could you tell me the correct usage? Very thanks! There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section: 1 2603 1 2619 1 2634 1 2635 1 2 1299 1942 1943 1917 1937 1939113 1937 1939114 - xiaodu My simulation system contains protein, dna and water. I used your script already for obtaining %exist hydrogen bonds between protein and dna-- 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] %hbond number problem
Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and the output info is nothing? So, could you tell me the correct usage? Very thanks! There are protein and sol in b4md.pdb file.The hbond.ndx file only contain the [ hbonds_Protein ] section: 1 2603 1 2619 1 2634 1 2635 1 2 1299 1942 1943 1917 1937 1939113 1937 1939114 - xiaodu -- 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] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?
Dear all I want to count all of the hydrogen bond's lifetime and donor-acceptor atoms in simulation,but I don't know how to do it. In many papers,the hydrogen bonds are list in this form: Donor Acceptor %Exist. ARG58 NH1 SOL2253OW21.663 ARG58 NH1 SOL7338OW0.160 ARG58NE SOL3595 OW 1.359 Can you give me some proposal? best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to countting Hbonds lifetime
Hi Erik and Justin Thanks for your reply. I want to obtain the HBond's permanence time.May be it's occupancies that you said. So,could you send me the script? Thank you very much. -- 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] Re: How to countting Hbonds lifetime
Hi Justin What is your means that the HBond's occupancy ? Can you tell me the difference about Hbonds lifetime and occupancy? I want to know which residues form the Hbond and the donor-acceptor atoms. The g_hbond can do it? Thank you very much. -- 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] ffamber03 RB dihedrals and amb2gmx.pl problem!
Hello all I obtained a top file after running the amb2gmx.pl script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that with the Ryckaert-Bellemans potential the 1-4 interactions must be excluded from the non-bonded list. So I think this top file is incorrect? Could you give me some opinion? Force field is amber03 in gmx4.5.1,ligand is disaccharide. Thanks ! -- 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] Re:gmx-users Digest, Vol 82, Issue 168
Hi all, If anyone have a script that amb2gmx_dihe.pl provide by Guillem Portella,could you send me a copy? Thanks very much!-- 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] ffamber03 RB dihedrals and amb2gmx.pl problem!
Hello all I obtained a top file after running the amb2gmx.pl script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that with the Ryckaert-Bellemans potential the 1-4 interactions must be excluded from the non-bonded list. So I think this top file is incorrect? Force field is amber03 in gmx4.5.1,ligand is disaccharide. Thanks ! -- 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] ffamber03 top file problem
Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate: --- Program grompp_m, VERSION 4.5.1 Source code file: toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROM··· I added some bonds and angles parameters like this: ·· ; residue 44 ASN rtp ASN q 0.0 664 N 44ASN N664 -0.430106 14.01 ; qtot 4.57 665 HD44ASN HD665 0.250466 2.016 ; qtot 4.824 666 CT 44ASN CA666 0.044609 12.01 ; qtot 4.869 ··· [ bonds ] ; aiaj functc0c1c2c3 ··· 676 678 1 678 679 1 0.10115 678 680 1 680 681 1 ··· [ angles ] ; aiajak functc0c1c2c3 648 650 652 1 651 650 652 1 115.149 650 652 653 1 650 652 654 1 Any help will highly appreciated!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topolbuild1_3 install problem
Hi, Mark, Thanks for the reply. You'are right,I forgot to enter the path.And my computer system is Ubuntu 10.04.I want to use the glycam force filed, then I type the command: software/topolbuild1_3/src/topolbuild -h I got the correct help information. But when I type this integral command: software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename it's error: *...@ubuntu:~$ software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename Fatal error. Source code file: atom_types.c, line: 87 Cannot open file software/topolbuild1_3/src/dat/parm/dat/antechamber/ATOMTYPE_GLYCAM.DEF Do you know how to solve this problem ? Thanks for you reply! xiaodu -- 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] glycam force field problem
Hi OliverI'm sorry to reply you so later.And I have some questions after reading your letter.You said that “The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”When you run grompp check in theoutput that fudge is set to 1.0.” Do you means to setting the fudgeLJ value to 1.0 in em.tpr file？I am not sure.I want to change this gromacs top files( all the output files by amb2gmx.pl converted) to gromacs itp files,then included in protein top file. And I plan to use the amber03 force filed. But I think that the [ defaults ] cannot included in itp files,or will cause an error about redifiniton.Because the [ defaults ] had exist in ”forcefield.itp.--;myt.itp [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5（ =1.0 ? ） 0.8333#define _FF_AMBER #define _FF_AMBER03 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333--So，do you know how to slove this problem？Can you give me some suggestion or a correct copy file by amb2gmx.pl converted? Thank you very much.My email address：gromacs...@126.comxiaodu -- 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] topolbuild1_3 install problem
Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. can anyone tell me to install the topolbuild1_3 correctly? Thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topolbuild1_3 install problem
Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. can anyone tell me to install the topolbuild1_3 correctly? Thank you! xiaodu -- 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] Re:gmx-users Digest, Vol 80, Issue 164
Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice? Thank your very much. all the best xiaodu - ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OHOH 0. 0. A 3.06647e-01 8.80314e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 HO 1ROHHO1 10.44500 1.00 2 OH 1ROH O1 2 -0.63900 16.00 3 CG 24GA C1 30.50900 12.00 4 H2 24GA H1 40.0 1.00 5 CG 24GA C2 50.24600 12.00 6 H1 24GA H2 60.0 1.00 7 OH 24GA O2 7 -0.71300 16.00 8 HO 24GAH2O 80.43700 1.00 9 CG 24GA C3 90.28600 12.00 10 H1 24GA H3 100.0 1.00 11 OH 24GA O3 11 -0.69900 16.00 12 HO 24GAH3O 120.42700 1.00 13 CG 24GA C4 130.25400 12.00 14 H1 24GA H4 140.0 1.00 15 CG 24GA C5 150.28300 12.00 16 H1 24GA H5 160.0 1.00 17 OS 24GA O5 17 -0.57400 16.00 18 CG 24GA C6 180.27600 12.00 19 H1 24GAH61 190.0 1.00 20 H1 24GAH62 200.0 1.00 21 OH 24GA O6 21 -0.68200 16.00 22 HO 24GAH6O 220.41800 1.00 23 OS 24GA O4 23 -0.46800 16.00 24 CG 30GA C1 240.50900 12.00 25 H2 30GA H1 250.0 1.00 26 CG 30GA C2 260.24600 12.00 27 H1 30GA H2 270.0 1.00 28 OH 30GA O2 28 -0.71300 16.00 29 HO 30GAH2O 290.43700 1.00 30 CG 30GA C3 300.28600 12.00 31 H1 30GA H3 310.0 1.00 32 OH 30GA O3 32 -0.69900 16.00 33 HO 30GAH3O 330.42700 1.00 34 CG 30GA C4 340.25400 12.00 35 H1 30GA H4 350.0 1.00 36 OH 30GA O4 36 -0.71000 16.00 37 HO 30GAH4O 370.43600 1.00 38 CG 30GA C5 380.28300 12.00 39 H1 30GA H5 390.0 1.00 40 OS 30GA O5 40 -0.57400 16.00 41 CG 30GA C6 410.27600 12.00 42 H1 30GAH61 420.0 1.00 43 H1 30GAH62 430.0 1.00 44 OH 30GA O6 44 -0.68200 16.00 45 HO 30GAH6O 450.41800 1.00 [ bonds ] ; aiaj funct r k 1 2 1 9.6000e-02 4.6275e+05 2122 1 9.6000e-02 4.6275e+05 1819 1 1.0900e-01 2.8451e+05 1820 1 1.0900e-01 2.8451e+05 1516 1 1.0900e-01 2.8451e+05 [ pairs ] ; aiaj funct 2 6 1 1 4 1 1 5 1 1 17 1 5 23 1 3 11 1 3 13 1 3 18 1 40 44 1 36 40 1 36
[gmx-users] amb2gmx.pl file
Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice? Thank your very much. all the best xiaodu - ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OHOH 0. 0. A 3.06647e-01 8.80314e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 HO 1ROHHO1 10.44500 1.00 2 OH 1ROH O1 2 -0.63900 16.00 3 CG 24GA C1 30.50900 12.00 4 H2 24GA H1 40.0 1.00 5 CG 24GA C2 50.24600 12.00 6 H1 24GA H2 60.0 1.00 7 OH 24GA O2 7 -0.71300 16.00 8 HO 24GAH2O 80.43700 1.00 9 CG 24GA C3 90.28600 12.00 10 H1 24GA H3 100.0 1.00 11 OH 24GA O3 11 -0.69900 16.00 12 HO 24GAH3O 120.42700 1.00 13 CG 24GA C4 130.25400 12.00 14 H1 24GA H4 140.0 1.00 15 CG 24GA C5 150.28300 12.00 16 H1 24GA H5 160.0 1.00 17 OS 24GA O5 17 -0.57400 16.00 18 CG 24GA C6 180.27600 12.00 19 H1 24GAH61 190.0 1.00 20 H1 24GAH62 200.0 1.00 21 OH 24GA O6 21 -0.68200 16.00 22 HO 24GAH6O 220.41800 1.00 23 OS 24GA O4 23 -0.46800 16.00 24 CG 30GA C1 240.50900 12.00 25 H2 30GA H1 250.0 1.00 26 CG 30GA C2 260.24600 12.00 27 H1 30GA H2 270.0 1.00 28 OH 30GA O2 28 -0.71300 16.00 29 HO 30GAH2O 290.43700 1.00 30 CG 30GA C3 300.28600 12.00 31 H1 30GA H3 310.0 1.00 32 OH 30GA O3 32 -0.69900 16.00 33 HO 30GAH3O 330.42700 1.00 34 CG 30GA C4 340.25400 12.00 35 H1 30GA H4 350.0 1.00 36 OH 30GA O4 36 -0.71000 16.00 37 HO 30GAH4O 370.43600 1.00 38 CG 30GA C5 380.28300 12.00 39 H1 30GA H5 390.0 1.00 40 OS 30GA O5 40 -0.57400 16.00 41 CG 30GA C6 410.27600 12.00 42 H1 30GAH61 420.0 1.00 43 H1 30GAH62 430.0 1.00 44 OH 30GA O6 44 -0.68200 16.00 45 HO 30GAH6O 450.41800 1.00 [ bonds ] ; aiaj funct r k 1 2 1 9.6000e-02 4.6275e+05 2122 1 9.6000e-02 4.6275e+05 1819 1 1.0900e-01 2.8451e+05 1820 1 1.0900e-01 2.8451e+05 1516 1 1.0900e-01 2.8451e+05 [ pairs ] ; aiaj funct 2 6 1 1 4 1 1 5 1 1 17 1 5 23 1 3 11 1 3 13 1 3 18 1 40 44 1 36 40 1 36
[gmx-users] amber convert gromacs input files
Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).? Many thanks! -- 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
