[gmx-users] NMR restrained MD
Justin Lemkul
jalemkul at vt.edu
Thu Sep 12 01:47:47 CEST 2013
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
> CN1 LC3 0.4000 1 15.0350
> CN2 LC3 0.4000 1 15.0350
> CN3 LC3 0.4000 1 15.0350
> NTM LNL -0.5000 1 14.0067
> CA LH2 0.3000 1 14.0270
> CB LC2 0.4000 1 14.0270
> OA LOS -0.8000 1 15.9994
> P LP 1.7000 1 30.9738
> OB LOM -0.8000 1 15.9994
> OC LOM -0.8000 1 15.9994
> OD LOS -0.7000 1 15.9994
> [ bonds ]
> ; ai aj funct c0 c1
> CN1 NTM 2 0.1470 8.7100e+06
> CN2 NTM 2 0.1470 8.7100e+06
> CN3 NTM 2 0.1470 8.7100e+06
> NTM CA 2 0.1470 8.7100e+06
> CA CB 2 0.1530 7.1500e+06
> CB OA 2 0.1430 8.1800e+06
> OA P 2 0.1610 4.8400e+06
> P OB 2 0.1480 8.6000e+06
> P OC 2 0.1480 8.6000e+06
> P OD 2 0.1610 4.8400e+06
> OD CC 2 0.1430 8.1800e+06
> [ angles ]
> ; ai aj ak funct angle fc
> CN1 NTM CN2 2 109.50 520.00
> CN1 NTM CN3 2 109.50 520.00
> CN1 NTM CA 2 109.50 520.00
> CN2 NTM CN3 2 109.50 520.00
> CN2 NTM CA 2 109.50 520.00
> CN3 NTM CA 2 109.50 520.00
> NTM CA CB 2 111.00 530.00
> CA CB OA 2 111.00 530.00
> CB OA P 2 120.00 530.00
> OA P OC 2 109.60 450.00
> OA P OB 2 109.60 450.00
> OA P OD 2 103.00 420.00
> [ dihedrals ]
> ; ai aj ak al funct ph0 cp mult
> CN3 NTM CA CB 1 0.00 3.77 3
> NTM CA CB OA 1 0.00 8.62 3
> CA CB OA P 1 0.00 3.77 3
> CB OA P OD 1 0.00 3.19 3
> OA P OD CC 1 0.00 3.19 3
> P OD CC CD 1 0.00 3.77 3
> OD CC CD CE 1 0.00 5.92 3
> CC CD OE C1A 1 0.00 3.77 3
> CC CD CE OG 1 0.00 5.92 3
> CD OE C1A C1B 1 180.00 24.00 2
> [ impropers ]
> ; GROMOS improper dihedrals
> ; ai aj ak al funct angle fc
> ; CD OE CE CC 2 35.26 334.72
> C1A OE OF C1B 2 0.00 167.36
> C2A OG OH C2B 2 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
> 263GLY HA1 2504 2.787 4.723 10.509
> 263GLY HA2 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
> 1DMPC CA 2518 4.511 3.404 3.857
> 1DMPC CB 2519 4.465 3.280 3.780
> 1DMPC OA 2520 4.576 3.195 3.752
> 1DMPC P 2521 4.533 3.055 3.686
> 1DMPC OB 2522 4.421 2.996 3.764
> 1DMPC OC 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.
Your .rtp format is wrong. The directives for bonded interactions do not
contain function types; these are specified in one line at the top of the .rtp
file. Consult manual section 5.6.1.
-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 at outerbanks.umaryland.edu | (410) 706-7441
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