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 1 3 1 1 3 1 0
[ DMPC ]
[ atoms ]
; ai Ber_type charge chgnr 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 2 14.0270
OA LOS -0.8000 2 15.9994
P LP 1.7000 2 30.9738
OB LOM -0.8000 2 15.9994
OC LOM -0.8000 2 15.9994
OD LOS -0.7000 2 15.9994
CC LC2 0.4000 3 14.0270
CD LH1 0.3000 3 13.0190
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
>> 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<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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> |
> (410)
> 706-7441
>
> ==============================**====================
> --
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