[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Thu Sep 12 17:03:53 CEST 2013
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 1 3 1 1 3 1 0
[ DMPC ]
[ atoms ]
; name type charge chgnr
CN1 LC3 0.4000 1
CN2 LC3 0.4000 1
CN3 LC3 0.4000 1
NTM LNL -0.5000 1
CA LH2 0.3000 1
CB LC2 0.4000 2
OA LOS -0.8000 2
P LP 1.7000 2
OB LOM -0.8000 2
OC LOM -0.8000 2
OD LOS -0.7000 2
[ bonds ]
; ai aj
CN1 NTM
CN2 NTM
CN3 NTM
NTM CA
CA CB
CB OA
OA P
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 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
P OD CC 2 120.00 530.00
OC P OB 2 120.00 780.00
OC P OD 2 109.60 450.00
[ 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
CD CE OG C2A 1 0.00 3.77 3
OE C1A C1B C1C 1 0.00 1.00 6
[ 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
Thanks
--Rama
On Thu, Sep 12, 2013 at 8:28 AM, Justin Lemkul <jalemkul at 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 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<http://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 .rtp file. Remember that the
> contents of an .rtp file are irrelevant once pdb2gmx is done.
>
>
> -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> | (410)
> 706-7441
>
> ==============================**====================
> --
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