On Fri, Sep 18, 2015 at 12:45 PM, Amber Maharaj <amber.maharaj.uoit.net>
wrote:
> Hi there,
>
> I am trying to run MD on a porphyrin molecule which is custom made. The
> porphyrin has a zinc center so antechamber doesn't handle it well. To work
> around this, I made a residue including the porphyrin without zinc and used
> antechamber to assign all the bonds, then I made an isolated zinc molecule
> (with coordinates at the center of the porphyrin) and manually assigned a
> charge in xleap. I then combined these in a pdb file as two different
> residues and manually added in bonds to the zinc atom.
>
The lack of specific details here makes it impossible to determine what
you *actually* did (versus what you thought you did or tried to do). I
would suggest working through some of the tutorials for learning how to
deal with parametrizing a new residue (zinc centers are more difficult than
those not containing a metal -- you may want to look at the MCPB tutorial
for parametrizing those).
I would suggest making sure you can do simpler systems with Amber before
trying to tackle this one. Try a pure system with no cofactor, then one
with a non-covalently bound ligand, then one with a custom residue
covalently bonded (e.g., tutorials B1, B4, and B5), before working to the
metal center tutorial (A20).
The minimization of the molecule seemed to work, but during the molecular
> dynamics nothing is happening and I am not sure why. I am a new AMBER user
> so I am not 100% sure I correctly assigned everything. Are there any issues
> in my approach? Any help would be much appreciated.
>
> Here is what I have in my input file for MD:
>
> MD for porphyrin unit
> &cntrl
> imin = 0,
> irest = 0,
> cut = 12.0,
> nstlim = 10000, dt = 0.001,
> ntpr = 1, ntwx = 1, ntwr = 1
> /
>
This input file has no thermostat, no final temperature, etc. You are
running constant energy dynamics (since ntt=0 by default, I think), where
the system is starting at absolute 0. The system will heat up as potential
energy is converted to kinetic energy, but the process will be fairly slow
and there is an upper limit to how hot the system can become without a
thermostat injecting energy.
The tutorials should help you create better input files and give you a
better understanding of the various options available to you.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2015 - 10:00:06 PDT
