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