Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
Hello Users, I am running mdrun for nsteps = 1000 ; 20 ns. Even though i have enough space on my cluster around 17 GB, I am getting the following error. *Cannot fsync 'md1.log'; maybe you are out of disk space?* What could be the reason for such errors. I am attaching my mdp file. Thanks in Advance. On Wed, Feb 26, 2014 at 6:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/26/14, 7:05 AM, lalithkumar wrote: Dear Dr. Justin, Thank you for pointing out the details of error. I have missed out the version of GROMACS I have been using and so I would like to let you know that my version is 4.5.7. In this version ffnonbonded.itp file of the gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I I doubt that's correct; every Gromacs version I've ever had contained [pairtypes] in this file. Check again. I don't have 4.5.7 installed anywhere, but in 4.6.x (several versions), it is clearly present. should agree that I dont know how they can be generated and to specify manually. So, in a crude way I can say that I have copied all the LJ 14 types from the ffG43a1p forcefield at the gromacs contributors link: http://www.gromacs.org/Downloads/User_contributions/Force_fields This includes the following addition lines: ; begin insert from pamac_hsnnb.itp ; [ pairtypes ] ; for LJ 14 - use same for OP as for OA OPO 1 0.0022619536 9.687375e-07 OP OM 1 0.0022619536 9.687375e-07 OP OP 1 0.0022619536 1.265625e-06 OW OP 1 0.0024331696 1.737e-06 N OP 1 0.0023475616 1.463625e-06 NT OP 1 0.0023475616 1.463625e-06 NL OP 1 0.0023475616 1.463625e-06 NR OP 1 0.0023475616 1.463625e-06 NZ OP 1 0.0023475616 1.463625e-06 NE OP 1 0.0023475616 1.463625e-06 C OP 1 0.0023009528 2.066625e-06 CH1 OP 1 0.0025663376 2.174625e-06 CH2 OP 1 0.0032687988 3.000375e-06 CH3 OP 1 0.0039370168 3.907125e-06 CH4 OP 1 0.005459888 6.59475e-06 CR1 OP 1 0.003536086 3.24675e-06 HC OP 1 0.000437552 1.38375e-07 H OP 1 0 0 DUM OP 1 0 0 S OP 1 0.0047521952 4.068e-06 CU1+ OP 1 0.000972602 8.053875e-08 CU2+ OP 1 0.000972602 8.053875e-08 FE OP 1 0 0 ZN2+ OP 1 0.000972602 1.09305e-07 MG2+ OP 1 0.0003842848 6.56775e-08 CA2+ OP 1 0.001507652 7.939125e-07 P OP 1 0.005773784 5.299875e-06 AR OP 1 0.003764374 3.53025e-06 F OP 1 0.0016322592 9.81225e-07 CL OP 1 0.0044525672 4.399875e-06 BR OP 1 0.0016332104 9.1035e-06 CMET OP 1 0.0044806276 5.1373125e-06 OMET OP 1 0.0022619536 1.265625e-06 NA+ OP 1 0.00040373684 1.63125e-07 CL- OP 1 0.0055883 1.16325e-05 CCHL OP 1 0.0024394475 2.268e-06 CLCHL OP 1 0.004334666 4.1738625e-06 HCHL OP 1 0.0002920184 7.377075e-08 SDMSO OP 1 0.0048877412 5.216175e-06 CDMSO OP 1 0.0045248108 5.2475625e-06 ODMSO OP 1 0.0022663291 9.752175e-07 CCL4 OP 1 0.0024394475 3.1014e-06 CLCL4 OP 1 0.0041472796 4.01985e-06 SI OP 1 0 0 ; end insert from pamac_hsnnb.itp And I had copied them as is to my ffnonbonded.itp file in modified gromos53a6.ff folder. Also, I have also modified atomtypes as per latest versions (for example CMET to CMet). Finally, I could pass the grompp set now and can run mdrun too successfully. Now I need your valuable review to know whether I had done is correct or can I do better than this way. If so please suggest some helping material regarding process of setting user defined LJ 14 pair types interactions to gromos53a6ff or any forcefield. And also, briefly comment on how difference with my results by doing in the method mentioned by me and with any other suggested method from your side. Please let me know if any further information to be provided from my side What you've done is not correct. You've made a mixed force field that is not necessarily viable. You need proper parameters within a single force field, not borrowed from some other parameter set, unless you can demonstrate through rigorous testing and validation that what you've done is correct. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201
Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
Dear Dr. Justin, Thank you for pointing out the details of error. I have missed out the version of GROMACS I have been using and so I would like to let you know that my version is 4.5.7. In this version ffnonbonded.itp file of the gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I should agree that I dont know how they can be generated and to specify manually. So, in a crude way I can say that I have copied all the LJ 14 types from the ffG43a1p forcefield at the gromacs contributors link: http://www.gromacs.org/Downloads/User_contributions/Force_fields This includes the following addition lines: ; begin insert from pamac_hsnnb.itp ; [ pairtypes ] ; for LJ 14 - use same for OP as for OA OPO 1 0.0022619536 9.687375e-07 OP OM 1 0.0022619536 9.687375e-07 OP OP 1 0.0022619536 1.265625e-06 OW OP 1 0.0024331696 1.737e-06 N OP 1 0.0023475616 1.463625e-06 NT OP 1 0.0023475616 1.463625e-06 NL OP 1 0.0023475616 1.463625e-06 NR OP 1 0.0023475616 1.463625e-06 NZ OP 1 0.0023475616 1.463625e-06 NE OP 1 0.0023475616 1.463625e-06 C OP 1 0.0023009528 2.066625e-06 CH1 OP 1 0.0025663376 2.174625e-06 CH2 OP 1 0.0032687988 3.000375e-06 CH3 OP 1 0.0039370168 3.907125e-06 CH4 OP 1 0.005459888 6.59475e-06 CR1 OP 1 0.003536086 3.24675e-06 HC OP 1 0.000437552 1.38375e-07 H OP 1 0 0 DUM OP 1 0 0 S OP 1 0.0047521952 4.068e-06 CU1+ OP 1 0.000972602 8.053875e-08 CU2+ OP 1 0.000972602 8.053875e-08 FE OP 1 0 0 ZN2+ OP 1 0.000972602 1.09305e-07 MG2+ OP 1 0.0003842848 6.56775e-08 CA2+ OP 1 0.001507652 7.939125e-07 P OP 1 0.005773784 5.299875e-06 AR OP 1 0.003764374 3.53025e-06 F OP 1 0.0016322592 9.81225e-07 CL OP 1 0.0044525672 4.399875e-06 BR OP 1 0.0016332104 9.1035e-06 CMET OP 1 0.0044806276 5.1373125e-06 OMET OP 1 0.0022619536 1.265625e-06 NA+ OP 1 0.00040373684 1.63125e-07 CL- OP 1 0.0055883 1.16325e-05 CCHL OP 1 0.0024394475 2.268e-06 CLCHL OP 1 0.004334666 4.1738625e-06 HCHL OP 1 0.0002920184 7.377075e-08 SDMSO OP 1 0.0048877412 5.216175e-06 CDMSO OP 1 0.0045248108 5.2475625e-06 ODMSO OP 1 0.0022663291 9.752175e-07 CCL4 OP 1 0.0024394475 3.1014e-06 CLCL4 OP 1 0.0041472796 4.01985e-06 SI OP 1 0 0 ; end insert from pamac_hsnnb.itp And I had copied them as is to my ffnonbonded.itp file in modified gromos53a6.ff folder. Also, I have also modified atomtypes as per latest versions (for example CMET to CMet). Finally, I could pass the grompp set now and can run mdrun too successfully. Now I need your valuable review to know whether I had done is correct or can I do better than this way. If so please suggest some helping material regarding process of setting user defined LJ 14 pair types interactions to gromos53a6ff or any forcefield. And also, briefly comment on how difference with my results by doing in the method mentioned by me and with any other suggested method from your side. Please let me know if any further information to be provided from my side Thank you With kind regards, Lalith -- View this message in context: http://gromacs.5086.x6.nabble.com/Adding-TPO-and-SEP-to-G53a6-Forcefield-tp5014706p5014824.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
On 2/26/14, 7:05 AM, lalithkumar wrote: Dear Dr. Justin, Thank you for pointing out the details of error. I have missed out the version of GROMACS I have been using and so I would like to let you know that my version is 4.5.7. In this version ffnonbonded.itp file of the gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I I doubt that's correct; every Gromacs version I've ever had contained [pairtypes] in this file. Check again. I don't have 4.5.7 installed anywhere, but in 4.6.x (several versions), it is clearly present. should agree that I dont know how they can be generated and to specify manually. So, in a crude way I can say that I have copied all the LJ 14 types from the ffG43a1p forcefield at the gromacs contributors link: http://www.gromacs.org/Downloads/User_contributions/Force_fields This includes the following addition lines: ; begin insert from pamac_hsnnb.itp ; [ pairtypes ] ; for LJ 14 - use same for OP as for OA OPO 1 0.0022619536 9.687375e-07 OP OM 1 0.0022619536 9.687375e-07 OP OP 1 0.0022619536 1.265625e-06 OW OP 1 0.0024331696 1.737e-06 N OP 1 0.0023475616 1.463625e-06 NT OP 1 0.0023475616 1.463625e-06 NL OP 1 0.0023475616 1.463625e-06 NR OP 1 0.0023475616 1.463625e-06 NZ OP 1 0.0023475616 1.463625e-06 NE OP 1 0.0023475616 1.463625e-06 C OP 1 0.0023009528 2.066625e-06 CH1 OP 1 0.0025663376 2.174625e-06 CH2 OP 1 0.0032687988 3.000375e-06 CH3 OP 1 0.0039370168 3.907125e-06 CH4 OP 1 0.005459888 6.59475e-06 CR1 OP 1 0.003536086 3.24675e-06 HC OP 1 0.000437552 1.38375e-07 H OP 1 0 0 DUM OP 1 0 0 S OP 1 0.0047521952 4.068e-06 CU1+ OP 1 0.000972602 8.053875e-08 CU2+ OP 1 0.000972602 8.053875e-08 FE OP 1 0 0 ZN2+ OP 1 0.000972602 1.09305e-07 MG2+ OP 1 0.0003842848 6.56775e-08 CA2+ OP 1 0.001507652 7.939125e-07 P OP 1 0.005773784 5.299875e-06 AR OP 1 0.003764374 3.53025e-06 F OP 1 0.0016322592 9.81225e-07 CL OP 1 0.0044525672 4.399875e-06 BR OP 1 0.0016332104 9.1035e-06 CMET OP 1 0.0044806276 5.1373125e-06 OMET OP 1 0.0022619536 1.265625e-06 NA+ OP 1 0.00040373684 1.63125e-07 CL- OP 1 0.0055883 1.16325e-05 CCHL OP 1 0.0024394475 2.268e-06 CLCHL OP 1 0.004334666 4.1738625e-06 HCHL OP 1 0.0002920184 7.377075e-08 SDMSO OP 1 0.0048877412 5.216175e-06 CDMSO OP 1 0.0045248108 5.2475625e-06 ODMSO OP 1 0.0022663291 9.752175e-07 CCL4 OP 1 0.0024394475 3.1014e-06 CLCL4 OP 1 0.0041472796 4.01985e-06 SI OP 1 0 0 ; end insert from pamac_hsnnb.itp And I had copied them as is to my ffnonbonded.itp file in modified gromos53a6.ff folder. Also, I have also modified atomtypes as per latest versions (for example CMET to CMet). Finally, I could pass the grompp set now and can run mdrun too successfully. Now I need your valuable review to know whether I had done is correct or can I do better than this way. If so please suggest some helping material regarding process of setting user defined LJ 14 pair types interactions to gromos53a6ff or any forcefield. And also, briefly comment on how difference with my results by doing in the method mentioned by me and with any other suggested method from your side. Please let me know if any further information to be provided from my side What you've done is not correct. You've made a mixed force field that is not necessarily viable. You need proper parameters within a single force field, not borrowed from some other parameter set, unless you can demonstrate through rigorous testing and validation that what you've done is correct. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
[gmx-users] Adding TPO and SEP to G53a6 Forcefield
Dear gromacs users, I have got two phosphorylated residues Tyrosine (TPO) and Serine (SEP) in A and B chains of my heterotrimer homology model. So, I went with the step by step process suggested by GROMACS at the link:http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Please dont mind, to be clear, I would like to place each and every single step that I have made and pasted in ff folder. 1. I copied a folder named gromos53a6.ff and file residuetypes.dat from the gromacs installed directory and pasted in the present working directory to trial the modifications. 2. I have added topologies for TPO and SEP to the .rtp file at the end of file as below: (I am very happy if anyone corrects me if there were any mistakes) [ TPO ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH1 0.0 2 OG1OA-0.5 2 P P 0.9 2 O1POP-0.8 2 O2POP-0.8 2 O3POP-0.8 2 CG2 CH3 0.0 3 C C 0.450 4 O O -0.450 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CB OG1gb_17 CB CG2gb_26 OG1 Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACB OG1 ga_12 CACB CG2 ga_14 OG1CB CG2 ga_14 CB OG1 P ga_25 OG1 P O1P ga_13 OG1 P O2P ga_13 OG1 P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 CB OG1 CG2CA gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACB OG1 gd_17 CACB OG1 P gd_14 CB OG1 P O1P gd_11 [ SEP ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 2 OGOA-0.5 2 P P 0.9 2 O1POP-0.8 2 O2POP-0.8 2 O3POP-0.8 2 C C 0.450 3 O O -0.450 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBOGgb_17 OG Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBOG ga_12 CBOG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBOG gd_17 CACBOG P gd_14 CBOG P O1P gd_11 3. Created an appropriate entries in .hdb files at the end of file for hydrogen addition TPO 1 1 1 H N -C CA SEP 1 1 1 H N -C CA 4. Addition of atom types in .atp file at the end OP 15.99940 ; phosphate oxygen (P=O) selon hansson aqvist jmb 97 and in ffnonbonded.itp file added: OP8 0.000 0.000 A 0.0022153 3.8239e-06 5. I dont think these are new bonded types and so not disturbed ffbonded.itp file. 6. Added TPO and SEP to residuetypes.dat file alphabetically and specifying it as protein 7. No special connectivity and so not edited specbond.dat After doing these steps, I called the forcefield within working directory while pdb2gmx prompted. No errors
Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
On 2/22/14, 6:31 AM, lalithkumar wrote: Dear gromacs users, I have got two phosphorylated residues Tyrosine (TPO) and Serine (SEP) in A and B chains of my heterotrimer homology model. So, I went with the step by step process suggested by GROMACS at the link:http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Please dont mind, to be clear, I would like to place each and every single step that I have made and pasted in ff folder. 1. I copied a folder named gromos53a6.ff and file residuetypes.dat from the gromacs installed directory and pasted in the present working directory to trial the modifications. 2. I have added topologies for TPO and SEP to the .rtp file at the end of file as below: (I am very happy if anyone corrects me if there were any mistakes) [ TPO ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH1 0.0 2 OG1OA-0.5 2 P P 0.9 2 O1POP-0.8 2 O2POP-0.8 2 O3POP-0.8 2 CG2 CH3 0.0 3 C C 0.450 4 O O -0.450 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CB OG1gb_17 CB CG2gb_26 OG1 Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACB OG1 ga_12 CACB CG2 ga_14 OG1CB CG2 ga_14 CB OG1 P ga_25 OG1 P O1P ga_13 OG1 P O2P ga_13 OG1 P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 CB OG1 CG2CA gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACB OG1 gd_17 CACB OG1 P gd_14 CB OG1 P O1P gd_11 [ SEP ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 2 OGOA-0.5 2 P P 0.9 2 O1POP-0.8 2 O2POP-0.8 2 O3POP-0.8 2 C C 0.450 3 O O -0.450 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBOGgb_17 OG Pgb_27 P O1Pgb_23 P O2Pgb_23 P O3Pgb_23 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBOG ga_12 CBOG P ga_25 OG P O1P ga_13 OG P O2P ga_13 OG P O3P ga_13 O1P P O2P ga_28 O1P P O3P ga_28 O2P P O3P ga_28 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBOG gd_17 CACBOG P gd_14 CBOG P O1P gd_11 3. Created an appropriate entries in .hdb files at the end of file for hydrogen addition TPO 1 1 1 H N -C CA SEP 1 1 1 H N -C CA 4. Addition of atom types in .atp file at the end OP 15.99940 ; phosphate oxygen (P=O) selon hansson aqvist jmb 97 and in ffnonbonded.itp file added: OP8 0.000 0.000 A 0.0022153 3.8239e-06 5. I dont think these are new bonded types and so not disturbed ffbonded.itp file. 6. Added TPO and SEP to residuetypes.dat file alphabetically and specifying it as protein 7. No special connectivity and so not edited specbond.dat After doing these steps, I called the forcefield within working directory while pdb2gmx prompted. No errors and my file got processed until genbox. The command issued was: g_pdb2gmx -ignh -f protein.pdb -o protein_pdb2gmx.pdb -p protein_topology.top -water
