AMBER Archive (2009)

Subject: [AMBER] protein protrudes from unit cell

From: Jeffrey (
Date: Wed Mar 18 2009 - 03:59:06 CDT

Dear amber users,

   I performed NPTsimulation (NTT=1) for a dimmer solvated in a truncated octahedral box, with a minimum distance of 10 angstrom from the atoms of protein to the edge of the solvent box. After about 5ns NPT simulation, the protein protruded from the unit cell. It seems that the protein didn't rotate around its center (geometry or center of mass), which caused the problem. Can the problem be avoided by translating and orienting center of the initial dimmer model to overlap with the origin of the coordinate set and then solvating it in the OCT box? Or this problem is due to the parameters used (DT, NSCM etc.)?

   Another surprising phenomena is that the ligand in one protein of the dimmer run away from the binding pocket while the other one kept in the original position of the other protein in the dimmer.

Here is the script I used in PMEMD:

NPT production
   ntx=5, irest=1,
   ntpr=100, ntwx=1000,ntwr=5000,
   dt=0.002,nstlim=1000000, nscm=5000,
   ntc=2, ntf=2,
   ntt=1, tautp=3.0,temp0=300.0,

Any suggestion is greatly appreciated.





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