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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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