Hi All,
I'm trying to simulate a protein in a mixture of water and octanol. I'm
done with the part of using antechamber to get the octanol parameters
and generate prmtop and inpcrd files for the protein in the mixed solvent.
The problem is how to edit those files to get pmemd to recognize the
solvent and its bounding box correctly. I've looked through the
tutorials and mailing list posts, but haven't found anything
particularly useful.
So far, I've added the following to the prmtop:
%FLAG
SOLVENT_POINTERS
%FORMAT(3I8)
220 20401 2
220 being the last residue of the protein, 20401 is the total number of
molecules and 2 is the starting index of the first solute molecule
(octanol).
I added the box information as the last line to inpcrd:
80.6719840 80.3103560 80.2556540 90.0000000 90.0000000 90.0000000
The first three being the box dimensions and the last three the angles
between the axes.
Minimization went fine, but during equilibration I got this message:
ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
For reference, my density equilibration input parameters are given below.
Is there another place in the input files that needs to be manually
edited or did I make incorrect additions?
Any advice would be much appreciated.
Sasha
protein: density
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
cut = 12,
ntr = 1,
ntp = 1,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ntt = 3,
gamma_ln = 2.0,
nstlim = 50000, dt = 0.001,
ntpr = 500, ntwx = 500, ntwr = 10000
/
Keep protein fixed with weak restraints
10.0
RES 1 220
END
END
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Received on Wed Apr 13 2011 - 16:00:02 PDT
