[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Thu Sep 12 00:19:17 CEST 2013
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.
I hope you can help me
--Thanks
Rama
--------------------------------------------------------------------------------====================
On Wed, Sep 11, 2013 at 9:16 AM, Rama Krishna Koppisetti <
ramkishna72 at 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 <jalemkul at 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 <jalemkul at 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 at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
>>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>>> 706-7441
>>>>
>>>> ==============================****====================
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>> --
>> ==============================**====================
>>
>> 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 <jalemkul at outerbanks.umaryland.edu>| (410)
>> 706-7441
>>
>> ==============================**====================
>> --
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