[gmx-users] NMR restrained MD

[Justin Lemkul]

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
>> -------------------------------------------------------
>>

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 | (410) 706-7441

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