[gmx-users] distance restraint in gromacs md run

[Justin Lemkul]

On 6/19/17 1:51 AM, Simon Kit Sang Chu wrote:
> Hi,
> 
> I have a protein of interest which requires distance restraint for C alpha
> atoms. However, the simulation does not seem to include the restraint at
> all.
> 
> *prod.mdp*
> define              = -DPOSRES
> constraints         =  none
> integrator          =  md
> dt                  =  0.005
> nsteps              =  40000000         ; 200 ns
> 
> 
> 
> *p1p2-merged.top*
> 
> ; Include forcefield parameters
> #include "ffPACE_1.3.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> Protein_A         3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>     chargeB      massB
>       1         N+      1    MET      N      1        0.7         17   ;
> qtot 0.7
> .
> .
> .
>   1861  1862  1863  1864     1
> 
> ; Include distance restraint file
> #ifdef POSRES
> #include "p1p2_dist.itp"
> #endif
> 
> *p1p2_dist.itp*
> ; distance restraints for r_1-62_r_115-176_&_C-alpha of FullP1P2 in water
> 
> [ distance_restraints ]
> ;   i     j ? label      funct         lo        up1        up2     weight
>      2    11 1     0          1   0.283898   0.483898     1.4839          1
>      2    17 1     1          1   0.552993   0.752993    1.75299          1
> .
> .
> .
> 
>   Do I need to use "define = -DDISTRES" and "ifdef DISPOSRES" instead? 

No, because you haven't enclosed your [distance_restraints] in any #ifdef block, 
so they are always active.

Is
> distance restraint only used in NMR refinement but not MD?
> 

No, they can be used during any process.  There are relevant .mdp options that 
must be set, though (see the manual).

How have you determined that the restraints aren't working?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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