[gmx-users] 11-cis retinal topology problem
Hello guys: I am building 11-cis-retinal topology these days. Here is what I did: first of all, I build a small peptide like compound which contains:11-cis-retinal connected to the protonated sidechain of LYS, ACE and NME capped the N-term and C-term of the LYS respectively. With this compound, I upload to paramchem and obtained a ligand.str file. Second, I merged the information (including BONDS, ANGLES and DIHEDRALS) of the ligand.str file into related section in par_all36_cgenff.prm. Then I run charmm2gromacs-pvm.py with command: python charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf it generate a folder called cgenff-2b7.ff which includes the following files: aminoacids.rtp ffbonded.itp forcefield.doc atomtypes.atp ffnonbonded.itp forcefield.itp I merged the content of above files into gromacs CHARMM36.ff and build a topology for 11-cis-retinal into aminoacids.rtp as following. This toplogy only contains informations for 11-cis-retinal and protonated LYS: - [ RETK ] [ atoms ] NNH1-0.470 HNH0.311 CACT10.072 HAHB0.093 CBCT2-0.184 HB1HA0.095 HB2HA0.096 CGCT2-0.187 HG1HA0.098 HG2HA0.099 CDCT2-0.1810 HD1HA0.0911 HD2HA0.0912 CECT20.2113 HE1HA0.0514 HE2HA0.0515 NZNH3-0.83216 HZ1HC0.4217 HZ2HC0.4218 CC0.5120 OO-0.5121 C1CG3010.00022 C2CG321-0.18223 C3CG321-0.17724 C4CG321-0.18325 C5CG2DC1-0.00126 C6CG2DC1-0.00127 C7CG2DC2-0.14928 C8CG2DC2-0.15029 C9CG2DC1-0.00330 C10CG2DC1-0.13431 C11CG321-0.19032 C12CG321-0.18733 C13CG2D1-0.00534 C14CG2D1-0.04335 C15CG3240.29936 C16CG331-0.26937 C17CG331 -0.26938 C18CG331 -0.26839 C19CG331 -0.26940 C20CG331 -0.26741 H7HGA40.15042 H8HGA40.15043 H10HGA40.15044 H14HGA40.15045 H21HGA20.09046 H22HGA20.09047 H31HGA20.09048 H32HGA20.09049 H41HGA20.09050 H42HGA20.09051 H111HGA20.09052 H112HGA20.09053 H121HGA20.09054 H122HGA20.09055 H151HGA20.09056 H152HGA20.09057 H161HGA30.09058 H162HGA30.09059 H163HGA30.09060 H171HGA30.09061 H172HGA30.09062 H173HGA30.09063 H181HGA30.09064 H182HGA30.09065 H183HGA30.09066 H191HGA30.09067 H192HGA30.09068 H193HGA30.09069 H201HGA30.09070 H202HGA30.09071 H203HGA30.09072 [ bonds ] CBCA CGCB CDCG CECD NZCE NHN NCA CCA C+N CAHA CBHB1 CBHB2 CGHG1 CGHG2 CDHD1 CDHD2 CEHE1 CEHE2 OC NZHZ1 NZHZ2 NZC15 C1C2 C1C6 C1C16 C1C17 C2C3 C2H21 C2H22 C3C4 C3H31 C3H32 C4C5 C4H41 C4H42 C5C6 C5C18 C6C7 C7C8 C7H7 C8C9 C8H8 C9C10 C9C19 C10C11 C10H10 C11C12 C11H111 C11H112 C12C13 C12H121 C12H122 C13C14 C13C20 C14C15 C14H14 C15H151 C15H152 C16H161 C16H162 C16H163 C17H171 C17H172 C17H173 C18H181 C18H182 C18H183 C19H191 C19H192 C19H193 C20H201 C20H202 C20H203 [ impropers ] N-CCAHN CCA+NO [ cmap ] -CNCAC+N - with the new forcefild, I run pdb2gmx: - pdb2gmx -f input.pdb -o gmx.pdb - it finished without any warnings or errors for this step. However, when I try to run grompp with command: - grompp_mpi -f em.mdp -c gmx.pdb -p topol.top - it failed with messages: - Program grompp_mpi, VERSION 4.6.2 Source code file: /home/albert/Desktop/gromacs-4.6.2/src/kernel/topdirs.c, line: 106 Fatal error: Invalid angle type 0 For
Re: [gmx-users] 11-cis retinal topology problem
Not directly. grompp does have the ability to pinpoint the current line, but nobody has extended that to this part of the code. You can hack in some crude output to src/kernel/topio.c and recompile if you want some clues where the issue arises. Change line 647 of that file to add the second line below. Then recompile and run. You should be able to just run grompp from your-cmake-build-dir/src/kernel/grompp (i.e. no need to install modified code). The last line it mentions should be where the problem exists. set_warning_line(wi, cpp_cur_file(handle), cpp_cur_linenr(handle)); warning_note(wi, Debugging); Mark On Sat, Jul 6, 2013 at 8:41 AM, Albert mailmd2...@gmail.com wrote: Hello guys: I am building 11-cis-retinal topology these days. Here is what I did: first of all, I build a small peptide like compound which contains:11-cis-retinal connected to the protonated sidechain of LYS, ACE and NME capped the N-term and C-term of the LYS respectively. With this compound, I upload to paramchem and obtained a ligand.str file. Second, I merged the information (including BONDS, ANGLES and DIHEDRALS) of the ligand.str file into related section in par_all36_cgenff.prm. Then I run charmm2gromacs-pvm.py with command: python charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf it generate a folder called cgenff-2b7.ff which includes the following files: aminoacids.rtp ffbonded.itp forcefield.doc atomtypes.atp ffnonbonded.itp forcefield.itp I merged the content of above files into gromacs CHARMM36.ff and build a topology for 11-cis-retinal into aminoacids.rtp as following. This toplogy only contains informations for 11-cis-retinal and protonated LYS: - [ RETK ] [ atoms ] NNH1-0.470 HNH0.311 CACT10.072 HAHB0.093 CBCT2-0.184 HB1HA0.095 HB2HA0.096 CGCT2-0.187 HG1HA0.098 HG2HA0.099 CDCT2-0.1810 HD1HA0.0911 HD2HA0.0912 CECT20.2113 HE1HA0.0514 HE2HA0.0515 NZNH3-0.83216 HZ1HC0.4217 HZ2HC0.4218 CC0.5120 OO-0.5121 C1CG3010.00022 C2CG321-0.18223 C3CG321-0.17724 C4CG321-0.18325 C5CG2DC1-0.00126 C6CG2DC1-0.00127 C7CG2DC2-0.14928 C8CG2DC2-0.15029 C9CG2DC1-0.00330 C10CG2DC1-0.13431 C11CG321-0.19032 C12CG321-0.18733 C13CG2D1-0.00534 C14CG2D1-0.04335 C15CG3240.29936 C16CG331-0.26937 C17CG331 -0.26938 C18CG331 -0.26839 C19CG331 -0.26940 C20CG331 -0.26741 H7HGA40.15042 H8HGA40.15043 H10HGA40.15044 H14HGA40.15045 H21HGA20.09046 H22HGA20.09047 H31HGA20.09048 H32HGA20.09049 H41HGA20.09050 H42HGA20.09051 H111HGA20.09052 H112HGA20.09053 H121HGA20.09054 H122HGA20.09055 H151HGA20.09056 H152HGA20.09057 H161HGA30.09058 H162HGA30.09059 H163HGA30.09060 H171HGA30.09061 H172HGA30.09062 H173HGA30.09063 H181HGA30.09064 H182HGA30.09065 H183HGA30.09066 H191HGA30.09067 H192HGA30.09068 H193HGA30.09069 H201HGA30.09070 H202HGA30.09071 H203HGA30.09072 [ bonds ] CBCA CGCB CDCG CECD NZCE NHN NCA CCA C+N CAHA CBHB1 CBHB2 CGHG1 CGHG2 CDHD1 CDHD2 CEHE1 CEHE2 OC NZHZ1 NZHZ2 NZC15 C1C2 C1C6 C1C16 C1C17 C2C3 C2H21 C2H22 C3C4 C3H31 C3H32 C4C5 C4H41 C4H42 C5C6 C5C18 C6C7 C7C8 C7H7 C8C9 C8H8 C9C10 C9C19 C10C11 C10H10 C11C12 C11H111 C11H112 C12C13 C12H121 C12H122 C13C14 C13C20 C14C15 C14H14 C15H151 C15H152 C16H161 C16H162 C16H163 C17H171
Re: [gmx-users] 11-cis retinal topology problem
On 07/06/2013 11:10 AM, Mark Abraham wrote: set_warning_line(wi, cpp_cur_file(handle), cpp_cur_linenr(handle)); warning_note(wi, Debugging); Mark Hello Mark: thanks a lot for kind messages. I changed above line in topio.c, set_warning_line(wi, cpp_cur_file(handle), cpp_cur_linenr(handle)); warning_note(wi, Debugging); but the compiling failed with messages: romacs-4.6.3/src/kernel/topio.c: In function ‘read_topol’: gromacs-4.6.3/src/kernel/topio.c:648:35: error: expected ‘)’ before ‘;’ token gromacs-4.6.3/src/kernel/topio.c:1014:9: error: expected ‘;’ before ‘}’ token make[2]: *** [src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o] Error 1 make[2]: *** Waiting for unfinished jobs thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 11-cis retinal topology problem
My bad. Use warning_note(wi, Debugging); On Sat, Jul 6, 2013 at 11:39 AM, Albert mailmd2...@gmail.com wrote: On 07/06/2013 11:10 AM, Mark Abraham wrote: set_warning_line(wi, cpp_cur_file(handle), cpp_cur_linenr(handle)); warning_note(wi, Debugging); Mark Hello Mark: thanks a lot for kind messages. I changed above line in topio.c, set_warning_line(wi, cpp_cur_file(handle), cpp_cur_linenr(handle)); warning_note(wi, Debugging); but the compiling failed with messages: romacs-4.6.3/src/kernel/topio.c: In function ‘read_topol’: gromacs-4.6.3/src/kernel/topio.c:648:35: error: expected ‘)’ before ‘;’ token gromacs-4.6.3/src/kernel/topio.c:1014:9: error: expected ‘;’ before ‘}’ token make[2]: *** [src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o] Error 1 make[2]: *** Waiting for unfinished jobs thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem in g_enemat in Gromacs 4.5.5
Hi Friends, I am working on peptide self assembly. I simulated two peptide which are random coil and apart from each other. As the time process they start to interact and form antiparallel beta sheet structure. My plan is to find the energy difference in random coil to beta shhet structure. I added protein1 protein2 group in mdp file I run g_energy coomand Output: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:protein1-protein1 51 LJ-SR:protein1-protein1 52 LJ-LR:protein1-protein1 53 Coul-14:protein1-protein1 54 LJ-14:protein1-protein1 55 Coul-SR:protein1-protein2 56 LJ-SR:protein1-protein2 57 LJ-LR:protein1-protein2 58 Coul-14:protein1-protein2 59 LJ-14:protein1-protein2 60 Coul-SR:protein1-rest 61 LJ-SR:protein1-rest 62 LJ-LR:protein1-rest 63 Coul-14:protein1-rest 64 LJ-14:protein1-rest 65 Coul-SR:protein2-protein2 66 LJ-SR:protein2-protein2 67 LJ-LR:protein2-protein2 68 Coul-14:protein2-protein2 69 LJ-14:protein2-protein2 70 Coul-SR:protein2-rest 71 LJ-SR:protein2-rest 72 LJ-LR:protein2-rest 73 Coul-14:protein2-rest 74 LJ-14:protein2-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein .But when I gave the command : g_enemat_mpi -f ../energy.edr -groups groups.dat -etot ener.xvg I ended with following Missery : Opened ../energy.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):protein1-protein1 (0,0)in energy file WARNING! could not find group (null):protein1-protein2 (0,1)in energy file group 1WARNING! could not find group (null):protein2-protein2 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 20 time 20.000 Will build energy half-matrix of 2 groups, 6 elements, over 21 frames Segmentation fault (core dumped) I will be thankful for any suggestion. Thank you in Advance. With 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] 11-cis retinal topology problem
On 07/06/2013 12:14 PM, Mark Abraham wrote: My bad. Use warning_note(wi, Debugging); thanks a lot Mark. I've obtained some informations now: Identified residue MET1 as a starting terminus. Warning: Residue RETK296 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue THR297 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue SER298 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue ALA299 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue VAL300 in chain has different type (Protein) from starting residue MET1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue ALA295 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: Fatal error: Residue 1 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- History has expired (PubMed Central) I take 11-cis-retinal SCHIFF base charmm format topology from the publication (Biophysical Journal, 83:3097-3112, 2002) from here: http://www.ks.uiuc.edu/Research/namd/wiki/?ParameterTopologyRepository and convert into gromacs .itp format: ; PROTONATED SCHIFF BASE [ RETK ] [ atoms ] NNH1-0.470000 HNH0.310001 CACT10.070002 HAHB0.090003 CC0.510004 OO-0.510005 CBCT2-0.180006 HB1HA0.090007 HB2HA0.090008 CGCT2-0.180009 HG1HA0.0900010 HG2HA0.0900011 CDCT2-0.1800012 HD1HA0.0900013 HD2HA0.0900014 CECT20.34015 HE1HA0.05016 HE2HA0.05017 N16NCH1-0.72718 H16HCR0.50519 C15CR150.36220 H15HPL10.18921 C14CR14-0.18022 H14HPL0.18023 C13CR130.13124 C20CT3-0.17025 H20AHA0.09026 H20BHA0.09027 H20CHA0.09028 C12CR12-0.11029 H12HPL0.11030 C11CR11-0.09031 H11HPL0.09032 C10CR10-0.10033 H10HPL0.10034 C9CR90.0035 C19CT3-0.2736 H19AHA0.0937 H19BHA0.0938 H19CHA0.0939 C8CR8-0.1040 H8HPL0.1041 C7CR7-0.1042 H7HPL0.1043 C6CR60.0044 C5CR50.0045 C18CT3-0.2746 H18AHA0.0947 H18BHA0.0948 H18CHA0.0949 C4CT2-0.2050 H4AHA0.1051 H4BHA0.1052 C3CT2-0.2053 H3AHA0.1054 H3BHA0.1055 C2CT2-0.2056 H2AHA0.1057 H2BHA0.1058 C1CT30.0059 C16CT3-0.2760 H16AHA0.0961 H16BHA0.0962 H16CHA0.0963 C17CT3-0.2764 H17AHA0.0965 H17BHA0.0966 H17CHA0.0967 [ bonds ] CBCA CGCB CDCG CECD N16CE NHN NCA OC CCA C+N CAHA CBHB1 CBHB2 CGHG1 CGHG2 CDHD1 CDHD2 CEHE1 CEHE2 C1C2 C1C6 C1C16 C1C17 C2C3 C2H2A C2H2B C3C4 C3H3A C3H3B C4C5 C4H4A C4H4B C5C6 C5C18 C6C7 C7C8 C7H7 C8C9 C8H8 C9C10 C9C19 C10C11 C10H10 C11C12 C11H11 C12C13 C12H12 C13C14 C13C20 C14C15 C14H14 C15N16 C15H15 N16H16 C16H16A C16H16B C16H16C C17H17A C17H17B C17H17C C18H18A C18H18B C18H18C C19H19A C19H19B C19H19C C20H20A C20H20B C20H20C [ impropers ] N-CCAHN CCA+NO C5C6C4C18 C6C1C5C7 C7C8C6H7 C8C7C9H8 C9C10C8C19 C10C9C11H10 C11C12C10H11 C12C11C13H12 C13
[gmx-users] new forcefield not appear in slave node pdb2gmx list
Hi all gromacs users, I have new forcefield and I have this folder in my working directory as well as in /share/gromacs/top. When I run pdb2gmx from head node this forcefield appears in list but when I run from slave nodes it do not appear in pdb2gmx list. could somebody tell me how do resolve this problem thanks in advance hari -- 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] new forcefield not appear in slave node pdb2gmx list
I think this question is for the developers of your operating system ... Dr. Vitaly V. Chaban On Sat, Jul 6, 2013 at 6:10 PM, Hari Pandey hariche...@yahoo.com wrote: Hi all gromacs users, I have new forcefield and I have this folder in my working directory as well as in /share/gromacs/top. When I run pdb2gmx from head node this forcefield appears in list but when I run from slave nodes it do not appear in pdb2gmx list. could somebody tell me how do resolve this problem thanks in advance hari -- 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] 11-cis retinal topology problem
On Sat, Jul 6, 2013 at 4:30 PM, Albert mailmd2...@gmail.com wrote: On 07/06/2013 12:14 PM, Mark Abraham wrote: My bad. Use warning_note(wi, Debugging); thanks a lot Mark. I've obtained some informations now: That's a completely different output. I think both your executables are broken, somehow. Clean the build and install trees and try again :-) Mark Identified residue MET1 as a starting terminus. Warning: Residue RETK296 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue THR297 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue SER298 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue ALA299 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue VAL300 in chain has different type (Protein) from starting residue MET1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue ALA295 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: Fatal error: Residue 1 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- History has expired (PubMed Central) I take 11-cis-retinal SCHIFF base charmm format topology from the publication (Biophysical Journal, 83:3097-3112, 2002) from here: http://www.ks.uiuc.edu/Research/namd/wiki/?ParameterTopologyRepository and convert into gromacs .itp format: ; PROTONATED SCHIFF BASE [ RETK ] [ atoms ] NNH1-0.470000 HNH0.310001 CACT10.070002 HAHB0.090003 CC0.510004 OO-0.510005 CBCT2-0.180006 HB1HA0.090007 HB2HA0.090008 CGCT2-0.180009 HG1HA0.0900010 HG2HA0.0900011 CDCT2-0.1800012 HD1HA0.0900013 HD2HA0.0900014 CECT20.34015 HE1HA0.05016 HE2HA0.05017 N16NCH1-0.72718 H16HCR0.50519 C15CR150.36220 H15HPL10.18921 C14CR14-0.18022 H14HPL0.18023 C13CR130.13124 C20CT3-0.17025 H20AHA0.09026 H20BHA0.09027 H20CHA0.09028 C12CR12-0.11029 H12HPL0.11030 C11CR11-0.09031 H11HPL0.09032 C10CR10-0.10033 H10HPL0.10034 C9CR90.0035 C19CT3-0.2736 H19AHA0.0937 H19BHA0.0938 H19CHA0.0939 C8CR8-0.1040 H8HPL0.1041 C7CR7-0.1042 H7HPL0.1043 C6CR60.0044 C5CR50.0045 C18CT3-0.2746 H18AHA0.0947 H18BHA0.0948 H18CHA0.0949 C4CT2-0.2050 H4AHA0.1051 H4BHA0.1052 C3CT2-0.2053 H3AHA0.1054 H3BHA0.1055 C2CT2-0.2056 H2AHA0.1057 H2BHA0.1058 C1CT30.0059 C16CT3-0.2760 H16AHA0.0961 H16BHA0.0962 H16CHA0.0963 C17CT3-0.2764 H17AHA0.0965 H17BHA0.0966 H17CHA0.0967 [ bonds ] CBCA CGCB CDCG CECD N16CE NHN NCA OC CCA C+N CAHA CBHB1 CBHB2 CGHG1 CGHG2 CDHD1 CDHD2 CEHE1 CEHE2 C1C2 C1C6 C1C16 C1C17 C2C3 C2H2A C2H2B C3C4 C3H3A C3H3B C4C5 C4H4A C4H4B C5C6 C5C18 C6C7 C7C8 C7H7 C8C9 C8H8 C9C10 C9C19 C10C11 C10H10 C11C12 C11H11 C12C13 C12H12 C13C14 C13C20 C14C15 C14H14 C15N16 C15H15 N16H16 C16H16A C16H16B C16H16C C17H17A C17H17B C17H17C C18H18A C18H18B C18H18C
Re: [gmx-users] new forcefield not appear in slave node pdb2gmx list
This could be helpful, I hope. http://www.gromacs.org/Documentation/File_Formats/FF.dat?highlight=change+ff+list Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273 De: Hari Pandey hariche...@yahoo.com Para: gmx-users@gromacs.org gmx-users@gromacs.org Enviado: sábado, 6 de julio de 2013 13:10 Asunto: [gmx-users] new forcefield not appear in slave node pdb2gmx list Hi all gromacs users, I have new forcefield and I have this folder in my working directory as well as in /share/gromacs/top. When I run pdb2gmx from head node this forcefield appears in list but when I run from slave nodes it do not appear in pdb2gmx list. could somebody tell me how do resolve this problem thanks in advance hari -- gmx-users mailing list gmx-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] Problem in g_enemat in Gromacs 4.5.5
On 7/6/13 8:21 AM, rama david wrote: Hi Friends, I am working on peptide self assembly. I simulated two peptide which are random coil and apart from each other. As the time process they start to interact and form antiparallel beta sheet structure. My plan is to find the energy difference in random coil to beta shhet structure. I added protein1 protein2 group in mdp file I run g_energy coomand Output: Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Temperature 15 Pres.-DC16 Pressure 17 Constr.-rmsd18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X48 Mu-Y 49 Mu-Z50 Coul-SR:protein1-protein1 51 LJ-SR:protein1-protein1 52 LJ-LR:protein1-protein1 53 Coul-14:protein1-protein1 54 LJ-14:protein1-protein1 55 Coul-SR:protein1-protein2 56 LJ-SR:protein1-protein2 57 LJ-LR:protein1-protein2 58 Coul-14:protein1-protein2 59 LJ-14:protein1-protein2 60 Coul-SR:protein1-rest 61 LJ-SR:protein1-rest 62 LJ-LR:protein1-rest 63 Coul-14:protein1-rest 64 LJ-14:protein1-rest 65 Coul-SR:protein2-protein2 66 LJ-SR:protein2-protein2 67 LJ-LR:protein2-protein2 68 Coul-14:protein2-protein2 69 LJ-14:protein2-protein2 70 Coul-SR:protein2-rest 71 LJ-SR:protein2-rest 72 LJ-LR:protein2-rest 73 Coul-14:protein2-rest 74 LJ-14:protein2-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein .But when I gave the command : g_enemat_mpi -f ../energy.edr -groups groups.dat -etot ener.xvg I ended with following Missery : Opened ../energy.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):protein1-protein1 (0,0)in energy file WARNING! could not find group (null):protein1-protein2 (0,1)in energy file group 1WARNING! could not find group (null):protein2-protein2 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 20 time 20.000 Will build energy half-matrix of 2 groups, 6 elements, over 21 frames Segmentation fault (core dumped) This problem has been posted several times before and looks buggy to me. Please open a redmine issue and provide a sample input file that reproduces the problem. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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] 11-cis retinal topology problem
On 7/6/13 4:17 PM, Mark Abraham wrote: On Sat, Jul 6, 2013 at 4:30 PM, Albert mailmd2...@gmail.com wrote: On 07/06/2013 12:14 PM, Mark Abraham wrote: My bad. Use warning_note(wi, Debugging); thanks a lot Mark. I've obtained some informations now: That's a completely different output. I think both your executables are broken, somehow. Clean the build and install trees and try again :-) Mark Identified residue MET1 as a starting terminus. Warning: Residue RETK296 in chain has different type (Other) from starting residue MET1 (Protein). Warning: Residue THR297 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue SER298 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue ALA299 in chain has different type (Protein) from starting residue MET1 (Protein). Warning: Residue VAL300 in chain has different type (Protein) from starting residue MET1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue ALA295 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: Fatal error: Residue 1 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This problem can be solved by remembering to complete step 5 of http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. As Mark notes, though, this issue is entirely separate from your initial problem. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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
