Re: [gmx-users] NMR restrained MD
Hi [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1311 3 1 0 [ DMPC ] [ atoms ] ;ai Ber_type charge chgnrmass CN1LC30.4000115.0350 CN2LC30.40001 15.0350 CN3LC30.4000115.0350 NTMLNL -0.5000114.0067 CALH20.3000114.0270 CBLC20.4000214.0270 OALOS -0.8000215.9994 P LP1.7000230.9738 OBLOM -0.8000215.9994 OCLOM -0.8000215.9994 ODLOS -0.7000215.9994 CCLC20.4000314.0270 CDLH10.3000313.0190 Now I'm trying to execute command to get ions.tpr file grompp -f minim.mdp -c conf_solv.gro -p topol.top -o ions.tpr Error encountered was: -- Program g_grompp, VERSION 4.5.5 Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks --Rama On Wed, Sep 11, 2013 at 6:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 6:19 PM, Rama Krishna Koppisetti wrote: Hi, I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid parameters [ DMPC ] [ atoms ] ;ai Ber_type charge resnr mass CN1LC30.4000115.0350 CN2LC30.40001 15.0350 CN3LC30.4000115.0350 NTMLNL -0.5000114.0067 CALH20.3000114.0270 CBLC20.4000114.0270 OALOS -0.8000115.9994 P LP1.7000130.9738 OBLOM -0.8000115.9994 OCLOM -0.8000115.9994 ODLOS -0.7000115.9994 [ bonds ] ; aiaj funct c0 c1 CN1 NTM2 0.1470 8.7100e+06 CN2 NTM2 0.1470 8.7100e+06 CN3 NTM2 0.1470 8.7100e+06 NTM CA2 0.1470 8.7100e+06 CA CB2 0.1530 7.1500e+06 CB OA2 0.1430 8.1800e+06 OAP2 0.1610 4.8400e+06 P OB2 0.1480 8.6000e+06 P OC2 0.1480 8.6000e+06 P OD2 0.1610 4.8400e+06 OD CC2 0.1430 8.1800e+06 [ angles ] ; ai aj ak funct angle fc CN1 NTM CN2 2109.50 520.00 CN1 NTM CN3 2109.50 520.00 CN1 NTMCA 2109.50 520.00 CN2 NTM CN3 2109.50 520.00 CN2 NTMCA 2109.50 520.00 CN3 NTMCA 2109.50 520.00 NTM CACB 2111.00 530.00 CA CBOA 2111.00 530.00 CB OA P 2120.00 530.00 OAPOC 2109.60 450.00 OAPOB 2109.60 450.00 OAPOD 2103.00 420.00 [ dihedrals ] ; ai aj ak al functph0 cpmult CN3 NTM CA CB1 0.00 3.773 NTM CA CB OA1 0.00 8.623 CA CB OAP1 0.00 3.773 CB OAP OD1 0.00 3.193 OAP OD CC1 0.00 3.193 P OD CC CD1 0.00 3.773 OD CC CD CE1 0.00 5.923 CC CD OE C1A1 0.00 3.773 CC CD CE OG1 0.00 5.923 CD OE C1A C1B1180.0024.002 [ impropers ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc ; CD OE CE CC2 35.26 334.72 C1A OE OF C1B2 0.00 167.36 C2A OG OH C2B2 0.00 167.36 I got a conf.gro file by using merge command pdb2gmx -f system.pdb -merge all Some part of the output file from above command 262TYR O 2500 2.592 4.761 10.187 263GLY N 2501 2.782 4.734 10.302 263GLY H 2502 2.879 4.719 10.299 263GLY CA 2503 2.716 4.747 10.431 263GLYHA1 2504 2.787 4.723 10.509 263GLYHA2 2505 2.635 4.677 10.435 263GLY C 2506 2.663 4.886 10.455 263GLY O1 2507 2.645 4.925 10.570 263GLY O2 2508 2.640 4.967 10.361 264ZN ZN 2509
Re: [gmx-users] NMR restrained MD
Hi, These are the parameters I kept in the .rtp file for DMPC molecule. Still getting same error message should I need to look at somewhere else. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1311 3 1 0 [ DMPC ] [ atoms ] ; nametypecharge chgnr CN1LC30.40001 CN2LC30.40001 CN3LC30.40001 NTMLNL -0.50001 CALH20.30001 CBLC20.40002 OALOS -0.80002 P LP1.70002 OBLOM -0.80002 OCLOM -0.80002 ODLOS -0.70002 [ bonds ] ; aiaj CN1 NTM CN2 NTM CN3 NTM NTM CA CA CB CB OA OAP P OB P OC P OD OD CC CC CD CD OE CD CE OE C1A [ angles ] ; ai aj ak funct angle fc CN1 NTM CN2 2109.50 520.00 CN1 NTM CN3 2109.50 520.00 CN1 NTMCA 2109.50 520.00 CN2 NTM CN3 2109.50 520.00 CN2 NTMCA 2109.50 520.00 CN3 NTMCA 2109.50 520.00 NTM CACB 2111.00 530.00 CA CBOA 2111.00 530.00 CB OA P 2120.00 530.00 OAPOC 2109.60 450.00 OAPOB 2109.60 450.00 OAPOD 2103.00 420.00 P ODCC 2120.00 530.00 OCPOB 2120.00 780.00 OCPOD 2109.60 450.00 [ dihedrals ] ; ai aj ak al functph0 cpmult CN3 NTM CA CB1 0.00 3.773 NTM CA CB OA1 0.00 8.623 CA CB OAP1 0.00 3.773 CB OAP OD1 0.00 3.193 OAP OD CC1 0.00 3.193 P OD CC CD1 0.00 3.773 OD CC CD CE1 0.00 5.923 CC CD OE C1A1 0.00 3.773 CC CD CE OG1 0.00 5.923 CD OE C1A C1B1180.0024.002 CD CE OG C2A1 0.00 3.773 OE C1A C1B C1C1 0.00 1.006 [ impropers ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc CD OE CE CC2 35.26 334.72 C1A OE OF C1B2 0.00 167.36 C2A OG OH C2B2 0.00 167.36 Thanks --Rama On Thu, Sep 12, 2013 at 8:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1311 3 1 0 [ DMPC ] [ atoms ] ;ai Ber_type charge chgnrmass CN1LC30.4000115.0350 CN2LC30.40001 15.0350 CN3LC30.4000115.0350 NTMLNL -0.5000114.0067 CALH20.3000114.0270 CBLC20.4000214.0270 OALOS -0.8000215.9994 P LP1.7000230.9738 OBLOM -0.8000215.9994 OCLOM -0.8000215.9994 ODLOS -0.7000215.9994 CCLC20.4000314.0270 CDLH10.3000313.0190 Now I'm trying to execute command to get ions.tpr file grompp -f minim.mdp -c conf_solv.gro -p topol.top -o ions.tpr Error encountered was: -- Program g_grompp, VERSION 4.5.5 Source code file: /builddir/build/BUILD/gromacs-** 4.5.5/src/kernel/toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- Given that it's the same error as before, either (1) you didn't fix the bonded directives within [DMPC] (not shown above) or (2) you did not re-create the topology with the corrected
Re: [gmx-users] NMR restrained MD
1. Did you re-run pdb2gmx after modifying the .rtp file? Yes.. I do run with modified .rtp file but output was same as previous. 2. Have you looked into the [bonds] directive in the .top file that pdb2gmx created to see if anything is out of place? Every line should have 5 entries: [bonds] directive contains only 3 entries for every line. atom_i atom_j funct b0 kb the entries present in [bonds] directive in the .top file was atom_i atom_j funct c0 c1 c2 c3. These are the some warnings for Zinc and calcium ions for pdb2gmx Warning: Residue ZN264 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue ZN265 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA266 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA267 in chain has different type (Ion) from starting residue PHE100 (Protein). Warning: Residue CA268 in chain has different type (Ion) from starting residue PHE100 (Protein). Thanks Justin .., I appreciate your help for whole week. I stopped here (give up). --Rama ___ Ramakrishna Koppisetti | Research Specialist | Protein NMR group | Biochemistry Department | University of Missouri | Columbia, USA | Email Id : koppiset...@missouri.edu | Mobile No : +573-529-5932 | ___ On Thu, Sep 12, 2013 at 11:27 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote: Hi, These are the parameters I kept in the .rtp file for DMPC molecule. Still getting same error message should I need to look at somewhere else. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1311 3 1 0 [ DMPC ] [ atoms ] ; nametypecharge chgnr CN1LC30.40001 CN2LC30.40001 CN3LC30.40001 NTMLNL -0.50001 CALH20.30001 CBLC20.40002 OALOS -0.80002 P LP1.70002 OBLOM -0.80002 OCLOM -0.80002 ODLOS -0.70002 [ bonds ] ; aiaj CN1 NTM CN2 NTM CN3 NTM NTM CA CA CB CB OA OAP P OB P OC P OD OD CC CC CD CD OE CD CE OE C1A If you don't specify bond lengths and force constants here, they need to be present in ffbonded.itp. Either approach is fine. The only issue you had before was that you included a function type, which would have explained the error you got before. [ angles ] ; ai aj ak funct angle fc CN1 NTM CN2 2109.50 520.00 CN1 NTM CN3 2109.50 520.00 CN1 NTMCA 2109.50 520.00 CN2 NTM CN3 2109.50 520.00 CN2 NTMCA 2109.50 520.00 CN3 NTMCA 2109.50 520.00 NTM CACB 2111.00 530.00 CA CBOA 2111.00 530.00 CB OA P 2120.00 530.00 OAPOC 2109.60 450.00 OAPOB 2109.60 450.00 OAPOD 2103.00 420.00 P ODCC 2120.00 530.00 OCPOB 2120.00 780.00 OCPOD 2109.60 450.00 Same as with [bonds], you cannot have a function type specified here. [ dihedrals ] ; ai aj ak al functph0 cpmult CN3 NTM CA CB1 0.00 3.773 NTM CA CB OA1 0.00 8.623 CA CB OAP1 0.00 3.773 CB OAP OD1 0.00 3.193 OAP OD CC1 0.00 3.193 P OD CC CD1 0.00 3.773 OD CC CD CE1 0.00 5.923 CC CD OE C1A1 0.00 3.773 CC CD CE OG1 0.00 5.923 CD OE C1A C1B1180.0024.002 CD CE OG C2A1 0.00 3.773 OE C1A C1B C1C1 0.00 1.006 [ impropers ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc CD OE CE CC2 35.26 334.72 C1A OE OF C1B2 0.00 167.36 C2A OG OH C2B2 0.00 167.36 Same applies for the dihedrals and impropers. To avoid another string of incomplete replies, please answer the following
Re: [gmx-users] NMR restrained MD
Hi Justin, Output topology from pdb2gmx. You could see some entries differ between two molecules. I'm looking forward to do restrained MD for this system by using Gromacs. [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 100 PHE rtp PHE q +1.0 1 opls_287100PHE N 1 -0.314.0067 ; qtot -0.3 2 opls_290100PHE H1 1 0.33 1.008 ; qtot 0.03 3 opls_290100PHE H2 1 0.33 1.008 ; qtot 0.36 4 opls_290100PHE H3 1 0.33 1.008 ; qtot 0.69 5 opls_293B100PHE CA 1 0.25 12.011 ; qtot 0.94 6 opls_140100PHE HA 1 0.06 1.008 ; qtot 1 7 opls_149100PHE CB 2 -0.005 12.011 ; qtot 0.995 ; residue 1 DMPC rtp DMPC q 0.0 2514LC3 1 DMPCCN18740.4 15.035 ; qtot 8.4 2515LC3 1 DMPCCN28740.4 15.035 ; qtot 8.8 2516LC3 1 DMPCCN38740.4 15.035 ; qtot 9.2 2517LNL 1 DMPCNTM874 -0.514.0067 ; qtot 8.7 2518LH2 1 DMPC CA8740.3 14.027 ; qtot 9 2519LC2 1 DMPC CB8750.4 14.027 ; qtot 9.4 2520LOS 1 DMPC OA875 -0.815.9994 ; qtot 8.6 2521 LP 1 DMPC P8751.730.9738 ; qtot 10.3 2522LOM 1 DMPC OB875 -0.815.9994 ; qtot 9.5 2523LOM 1 DMPC OC875 -0.815.9994 ; qtot 8.7 2524LOS 1 DMPC OD875 -0.715.9994 ; qtot 8 2525LC2 1 DMPC CC8760.4 14.027 ; qtot 8.4 2526LH1 1 DMPC CD8760.3 13.019 ; qtot 8.7 2527LOS 1 DMPC OE876 -0.715.9994 ; qtot 8 [ bonds ] ; aiaj functc0c1c2c3 ;bonds for protein 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 521 1 7 8 1 7 9 1 710 1 ;bonds from lipid atoms 2514 2517 1 0.1470 8.7100e+06 2515 2517 1 0.1470 8.7100e+06 2516 2517 1 0.1470 8.7100e+06 2517 2518 1 0.1470 8.7100e+06 2518 2519 1 0.1530 7.1500e+06 2519 2520 1 0.1430 8.1800e+06 2520 2521 1 0.1610 4.8400e+06 [ pairs ] ; aiaj functc0c1c2c3 1 8 1 1 9 1 110 1 122 1 123 1 2 6 1 2 7 1 221 1 3 6 1 3 7 1 321 1 4 6 1 4 7 1 421 1 511 1 513 1 [ angles ] ; aiajak functc0c1 c2c3 ;angles for protein atoms 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 1 5 6 1 1 5 7 1 1 521 1 6 5 7 1 6 521 1 ;angles for lipid atoms 2514 2517 2515 1109.50 520.00 2514 2517 2516 1109.50 520.00 2514 2517 2518 1109.50 520.00 2515 2517 2516 1 109.50 520.00 2515 2517 2518 1109.50 520.00 2516 2517 2518 1109.50 520.00 2517 2518 2519 1111.00 530.00 2518 2519 2520 1111.00 530.00 2519 2520 2521 1120.00 530.00 2520 2521 2522 1109.60 450.00 [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 ;For protein 2 1 5 6 3 2 1 5 7 3 2 1 521 3 23252730 3dih_ARG_chi1_N_C_C_C 45252730 3dih_ARG_chi1_C_C_C_CO ;For lipids 2516 2517 2518 2519 31 0.00 3.773 2514 2517 2518 2519 3 2515 2517 2518 2519 3 2517 2518 2519 2520 31 0.00 8.623 2518 2519 2520 2521 31 0.00 3.773 2519 2520 2521 2524 31 0.00 3.193 2519 2520 2521 2522 3 2519 2520 2521 2523 3 2520 2521 2524 2525 31 0.00 3.193 Thanks --Rama == On Thu, Sep 12, 2013 at 12:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/12/13 1:17 PM, Rama Krishna Koppisetti wrote: 1. Did you re-run pdb2gmx after modifying the .rtp file? Yes.. I do run
Re: [gmx-users] NMR restrained MD
Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. I'm getting an Error message like, ERROR 18815 [file topol.top, line 54180]: No default Ryckaert-Bell. types ERROR 18816 [file topol.top, line 54181]: No default Ryckaert-Bell. types --Rama On Tue, Sep 10, 2013 at 5:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 6:10 PM, Rama Krishna Koppisetti wrote: Hi, How to convert normal dihedrals to so-called Ryckaert-Bellemans potential dihedrals. Is there any script available for that. Periodic dihedrals and R-B dihedrals have different functional forms. See the manual. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi Justin, These type of dihedrals I'm using now, Is it correct format. [ dihedral s ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc LH1 LOS LC2 LC22 35.26 334.72 LC LOS LO LP22 0.00 167.36 LC LOS LO LP22 0.00 167.36 [ dihedral s ] ; ai aj ak al functph0 cLP mult LC3 LNL LH2 LC21 0.00 3.773 LNL LH2 LC2 LOS1180.00 5.861 LH2 LC2 LOSLP1 0.00 3.773 LC2 LOSLP LOS1 0.00 3.193 LP LOS LC2 LH11 0.00 3.773 LOS LC2 LH1 LC21 0.00 5.923 LC2 LH1 LOSLC1 0.00 3.773 T hanks Rama On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. You should use whatever the force field tells you. I'm getting an Error message like, ERROR 18815 [file topol.top, line 54180]: No default Ryckaert-Bell. types ERROR 18816 [file topol.top, line 54181]: No default Ryckaert-Bell. types What are the dihedrals on these lines? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Those lines are related to DMPC lipid dihedrals. -_Rama On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. You should use whatever the force field tells you. I'm getting an Error message like, ERROR 18815 [file topol.top, line 54180]: No default Ryckaert-Bell. types ERROR 18816 [file topol.top, line 54181]: No default Ryckaert-Bell. types What are the dihedrals on these lines? -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Sorry.., Justin Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are coming from all DMPC atoms dihedrals only not by protein dihedrals. --Rama On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote: Those lines are related to DMPC lipid dihedrals. I know that much. I am trying to extract some actual detail here so I can help you reach a conclusion. The error indicates line numbers in the topology. On those line numbers are a sequence of atom numbers, which can be mapped back to atom types. I'm asking you what that specific information is. -Justin On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. You should use whatever the force field tells you. I'm getting an Error message like, ERROR 18815 [file topol.top, line 54180]: No default Ryckaert-Bell. types ERROR 18816 [file topol.top, line 54181]: No default Ryckaert-Bell. types What are the dihedrals on these lines? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi, I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid parameters [ DMPC ] [ atoms ] ;ai Ber_type charge resnr mass CN1LC30.4000115.0350 CN2LC30.40001 15.0350 CN3LC30.4000115.0350 NTMLNL -0.5000114.0067 CALH20.3000114.0270 CBLC20.4000114.0270 OALOS -0.8000115.9994 P LP1.7000130.9738 OBLOM -0.8000115.9994 OCLOM -0.8000115.9994 ODLOS -0.7000115.9994 [ bonds ] ; aiaj funct c0 c1 CN1 NTM2 0.1470 8.7100e+06 CN2 NTM2 0.1470 8.7100e+06 CN3 NTM2 0.1470 8.7100e+06 NTM CA2 0.1470 8.7100e+06 CA CB2 0.1530 7.1500e+06 CB OA2 0.1430 8.1800e+06 OAP2 0.1610 4.8400e+06 P OB2 0.1480 8.6000e+06 P OC2 0.1480 8.6000e+06 P OD2 0.1610 4.8400e+06 OD CC2 0.1430 8.1800e+06 [ angles ] ; ai aj ak funct angle fc CN1 NTM CN2 2109.50 520.00 CN1 NTM CN3 2109.50 520.00 CN1 NTMCA 2109.50 520.00 CN2 NTM CN3 2109.50 520.00 CN2 NTMCA 2109.50 520.00 CN3 NTMCA 2109.50 520.00 NTM CACB 2111.00 530.00 CA CBOA 2111.00 530.00 CB OA P 2120.00 530.00 OAPOC 2109.60 450.00 OAPOB 2109.60 450.00 OAPOD 2103.00 420.00 [ dihedrals ] ; ai aj ak al functph0 cpmult CN3 NTM CA CB1 0.00 3.773 NTM CA CB OA1 0.00 8.623 CA CB OAP1 0.00 3.773 CB OAP OD1 0.00 3.193 OAP OD CC1 0.00 3.193 P OD CC CD1 0.00 3.773 OD CC CD CE1 0.00 5.923 CC CD OE C1A1 0.00 3.773 CC CD CE OG1 0.00 5.923 CD OE C1A C1B1180.0024.002 [ impropers ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc ; CD OE CE CC2 35.26 334.72 C1A OE OF C1B2 0.00 167.36 C2A OG OH C2B2 0.00 167.36 I got a conf.gro file by using merge command pdb2gmx -f system.pdb -merge all Some part of the output file from above command 262TYR O 2500 2.592 4.761 10.187 263GLY N 2501 2.782 4.734 10.302 263GLY H 2502 2.879 4.719 10.299 263GLY CA 2503 2.716 4.747 10.431 263GLYHA1 2504 2.787 4.723 10.509 263GLYHA2 2505 2.635 4.677 10.435 263GLY C 2506 2.663 4.886 10.455 263GLY O1 2507 2.645 4.925 10.570 263GLY O2 2508 2.640 4.967 10.361 264ZN ZN 2509 4.326 3.894 9.500 265ZN ZN 2510 4.221 3.718 8.159 266CA CA 2511 4.917 3.016 8.702 267CA CA 2512 3.073 4.064 8.337 268CA CA 2513 4.476 2.192 8.391 1DMPC CN1 2514 4.712 3.345 3.963 1DMPC CN2 2515 4.507 3.298 4.076 1DMPC CN3 2516 4.587 3.524 4.058 1DMPC NTM 2517 4.576 3.394 3.989 1DMPCCA 2518 4.511 3.404 3.857 1DMPCCB 2519 4.465 3.280 3.780 1DMPCOA 2520 4.576 3.195 3.752 1DMPC P 2521 4.533 3.055 3.686 1DMPCOB 2522 4.421 2.996 3.764 1DMPCOC 2523 4.528 3.081 3.540 Now I'm trying to execute command to get ions.tpr file grompp -f minim.mdp -c conf_solv.gro -p topol.top -o ions.tpr Error encountered was: -- Program g_grompp, VERSION 4.5.5 Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c, line: 1631 Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried to look all the parameters in the .rtp file and ffbonded.itp and ffnonbonded.itp files I don't find any mistake. I hope you can help me --Thanks Rama On Wed, Sep 11, 2013 at 9:16 AM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Sorry.., Justin Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are coming from all DMPC atoms dihedrals only not by protein dihedrals. --Rama On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote: Those lines are related to DMPC lipid dihedrals. I know that much. I am trying to extract some actual detail here so I can help you reach
Re: [gmx-users] NMR restrained MD
Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Thanks --Rama On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi Justin, There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is there any suggestions from you. WARNING 1 [file ffbonded.itp, line 2817]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 5.86 1 180 5.86 1 new: LNL LH2 LC2 LOS1 0.00 8.623 WARNING 2 [file ffbonded.itp, line 2820]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LC2 LOSLP LOS1 0.00 3.193 WARNING 3 [file ffbonded.itp, line 2821]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 3.19 3 0 3.19 3 new: LOSLP LOS LC21 0.00 5.092 WARNING 4 [file ffbonded.itp, line 2822]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LOSLP LOS LC21 0.00 3.193 Thanks --Rama On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can be a little bit of a pain, you could instead change the atom types in the molecule parameter, to ones that have defined angles and bond types with each other. Of course, you would need to make sure that you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. Check out ffbonded in the appropriate forcefield folder to see which atomtypes have defined bond types. Check out atomtypes.atp to see all the atom types for the forcefield Given that at present the issue involves only protein and lipids, the approach of swapping around atom types is very dangerous, probably more so than assigning bonded parameters by analogy. I don't recall the OP ever telling us what the force field is, though, so it's hard to know all of what we're dealing with here. -Justin On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Go to the line number in the .top indicated in the error message and determine the atom types. This will tell you the sequence of atom types involved in the R-B dihedral that is missing. In theory, you would then add missing parameters to ffbonded.itp, if they exist. -Justin On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error while running energy minimization: what to do for these type of errors. They're exactly the same as the dihedral error from before. You're using parameters that don't exist in the force field. -Justin ERROR 218 [file topol.top, line 23487]: No default Ryckaert-Bell. types ERROR 219 [file topol.top, line 23499]: No default Ryckaert-Bell. types ERROR 220 [file topol.top, line 23500]: No default Ryckaert-Bell. types ERROR 221 [file topol.top, line 23501]: No default Ryckaert-Bell. types ERROR 222 [file topol.top, line 23502]: No default Ryckaert-Bell. types ERROR 223 [file topol.top, line 23503]: No default Ryckaert-Bell. types ERROR 224 [file topol.top, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org
Re: [gmx-users] NMR restrained MD
Hi, How to convert normal dihedrals to so-called Ryckaert-Bellemans potential dihedrals. Is there any script available for that. Thanks Rama On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote: H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Presumably you are following Chris Neale's half-epsilon, double pairlist method then? In any case, you're defining the same interaction multiple times using different parameters. Something has gone wrong somewhere along the way. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Thanks --Rama On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: -- 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] NMR restrained MD
Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif
Re: [gmx-users] NMR restrained MD
Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include Distance restraints file #ifdef DISRES #include beta_disres.itp #endif ; Strong position restraints for InflateGRO #ifdef
Re: [gmx-users] NMR restrained MD
Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. Thanks --Rama On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. The force field does not have parameters for whatever dihedral is listed on line 55130 in the topology. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. Thanks --Rama On Mon, Sep 9, 2013 at 1:57 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity
Re: [gmx-users] NMR restrained MD
Hi Justin, I use similar procedure as you mentioned in the tutorial to generate my topologies for protein and bilayer. there is no .rtp file for lipid. Is there any reference to include lipid molecule in aminoacid.rtp file. Thanks Rama On Fri, Sep 6, 2013 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:56 PM, Rama Krishna Koppisetti wrote: Hi Justin , Is there any script available in gromacs documentation or some where? My guess is no. Ask Google. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Hi Justin, If you are willing to see my complex pdb file or complex .gro file and topology files, I'll send you for the reference. Thanks Rama On Sat, Sep 7, 2013 at 5:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/7/13 6:40 PM, Rama Krishna Koppisetti wrote: Hi Justin, I use similar procedure as you mentioned in the tutorial to generate my topologies for protein and bilayer. there is no .rtp file for lipid. Is there any reference to include lipid molecule in aminoacid.rtp file. Read the manual and look at existing examples. The .rtp format is very similar to the standard topology (.top/.itp) format, probably even a bit more straightforward. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] NMR restrained MD
Sorry ..,here are my distance restraints file: [ distance_restraints ] ;ai ajtypeindextype'low up1up2fac 3012679 1 0 1 0.0 1.62142.2111.0 3012696 1 0 10.0 1.62142.2111.0 3013415 1 0 10.0 1.62142.2111.0 301 3432 1 0 10.0 1.62142.211 1.0 3016635 1 0 1 0.0 1.62142.211 1.0 301 6652 1 0 10.0 1.62142.2111.0 3017187 1 0 10.0 1.62142.2111.0 3017204 1 0 10.0 1.62142.2111.0 301 7279 1 0 1 0.0 1.62142.2111.0 301 7296 1 0 1 0.0 1.62142.2111.0 301 7371 1 0 1 0.0 1.62142.2111.0 3017388 1 0 10.0 1.62142.2111.0 301 7923 1 0 1 0.0 1.62142.2111.0 3017940 1 0 10.0 1.62142.2111.0 3018199 1 0 10.0 1.62142.2111.0 3018216 1 0 1 0.0 1.62142.2111.0 3442679 1 1 1 0.0 1.57632.14951.0 3442696 1 1 10.0 1.57632.14951.0 3443415 1 1 10.0 1.57632.14951.0 344 3432 1 1 10.0 1.57632.14951.0 3446635 1 1 1 0.0 1.57632.14951.0 344 6652 1 1 10.0 1.57632.14951.0 3447187 1 1 10.0 1.57632.14951.0 3447204 1 1 10.0 1.57632.14951.0 344 7279 1 1 1 0.0 1.57632.14951.0 344 7296 1 1 1 0.0 1.57632.14951.0 344 7371 1 1 1 0.0 1.57632.14951.0 3447388 1 1 10.0 1.57632.14951.0 344 7923 1 1 1 0.0 1.57632.14951.0 3447940 1 1 10.0 1.57632.14951.0 3448199 1 1 10.0 1.57632.14951.0 3448216 1 1 1 0.0 1.57632.14951.0 8892679 1 2 1 0.0 1.83042.4961.0 8892696 1 2 10.0 1.83042.4961.0 8893415 1 2 10.0 1.83042.4961.0 889 3432 1 2 10.0 1.83042.4961.0 8896635 1 2 1 0.0 1.83042.4961.0 889 6652 1 2 10.0 1.83042.4961.0 8897187 1 2 10.0 1.83042.4961.0 8897204 1 2 10.0 1.83042.4961.0 889 7279 1 2 1 0.0 1.83042.4961.0 889 7296 1 2 1 0.0 1.83042.4961.0 889 7371 1 2 1 0.0 1.83042.4961.0 8897388 1 2 10.0 1.83042.4961.0 889 7923 1 2 1 0.0 1.83042.4961.0 8897940 1 2 10.0 1.83042.4961.0 8898199 1 2 10.0 1.83042.4961.0 8898216 1 2 1 0.0 1.83042.4961.0 9222679 1 3 1 0.0
Re: [gmx-users] NMR restrained MD
H i Justin, Thanks for your reply. How to do that? On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include Distance restraints file #ifdef DISRES #include beta_disres.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DMPC topology #include ramaLJ.ff/dmpcLJ.itp ; Include water topology #include ramaLJ.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ramaLJ.ff/ions.itp [ system ] ; Name Giving Russians Opium May Alter Current Situation in water [ molecules ] ; Compound#mols Protein1 DMPC
Re: [gmx-users] NMR restrained MD
Hi Justin , Is there any script available in gromacs documentation or some where? Thanks On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include Distance restraints file #ifdef DISRES #include beta_disres.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES
Re: [gmx-users] snapshot
Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] snapshot
Thank you very much *Justin*. -- Rama On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep The interval depends on how often you saved snapshots. You do not need -dt and -dump options. You will get separate coordinate files with -sep and the correct value of -skip will give you what you want. If you saved a frame every 50 ps, then trjconv -skip 5 -sep will give you a frame every 250 ps. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Re: snapshot
Thanks *Thomas* --Rama On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier schl...@uni-mainz.dewrote: Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets overwritten by '-dt 250') the additional use of '-dump x' might be the problem, since with '-dump x' GMX writes only the frame at time x Greetings Thomas Am 15.07.2013 15:03, schrieb gmx-users-requ...@gromacs.org: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Ramaramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] How to make changes on Trajectory file?
O kay... T hanks for prompt reply *Justin* * . --Rama ** * On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 12:08 PM, Rama wrote: Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. You can't create frames that aren't there. You can decrease the frame interval using trjconv -skip, but you can't perform magic the other way around. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Stimulation stopped at 2ns
Thanks Justin for your reply, I found something like this, in .log file,nsteps=100 but in .mdp file it is nsteps=500. I don't see any stdout and stderr files. ___ On Mon, Jul 8, 2013 at 3:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/8/13 4:33 PM, Rama wrote: Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where. There is nothing in the .mdp file that would cause the run to stop. Either the simulation is crashing or you have some queuing system that is terminating the job. Check stdout, stderr, and .log file(s) for information. -Justin Thanks in Advance. - title = Protein-DMPC bilayer Production MD ; Run parameters integrator = md; leap-frog integrator nsteps = 500 ; 2 * 500 = 1 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 10; save coordinates every 200 ps nstvout = 10; save velocities every 200 ps nstxtcout = 5 ; xtc compressed trajectory output every 100 ps nstenergy = 5 ; save energies every 100 ps nstlog = 10; update log file every 200 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = CA_ZN_DMPC_ProteinSOL_CL ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL -- View this message in context: http://gromacs.5086.x6.nabble.** com/Stimulation-stopped-at-**2ns-tp5009669.htmlhttp://gromacs.5086.x6.nabble.com/Stimulation-stopped-at-2ns-tp5009669.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- ==** 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list
Re: [gmx-users] Distance restraints
Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.comwrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Distance restraints
Hi..,Mark but it is within the same molecule , not in inter-molecules. On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Yes. Check out the manual first! Mark On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Mark, Is there anyway to define NMR distance restraints in MD simulations to do refinement for the complex structure. On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: You can't - the atoms must be part of the same [moleculetype]. The good news is that a [moleculetype] can have whatever you want in it, so you can have more than one molecule. The bad news is that you'll have to be cunning with renumbering atoms in the merged [moleculetype] and there's no tools that do that. (Or maybe there's a smart-alec trick using the pull code, but I have no idea what.) Mark On Tue, May 21, 2013 at 4:20 PM, Rama ramkishn...@gmail.com wrote: Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 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
