[gmx-users] NMR restrained MD

[Justin Lemkul]

On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote:
> 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

If you don't specify bond lengths and force constants here, they need to be 
present in ffbonded.itp.  Either approach is fine.  The only issue you had 
before was that you included a function type, which would have explained the 
error you got before.

>   [ 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

Same as with [bonds], you cannot have a function type specified here.

>   [ 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
>

Same applies for the dihedrals and impropers.

To avoid another string of incomplete replies, please answer the following 
questions directly.  Remember, I'm trying (very hard) to help you resolve this 
and we're just spinning our wheels.

1. Did you re-run pdb2gmx after modifying the .rtp file?
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx 
created to see if anything is out of place?  Every line should have 5 entries:

atom_i  atom_j  funct  b0  kb

Anything more or less (in this case) is wrong.  Can you identify any problematic 
lines, and if so, to which atoms do they apply?

-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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