Dear Amber Users
I am trying to do MD using implicit solvent models on a protein that
contains a heme iron.
Using, in-vacuo, 8.0 angstrom cutoff, the distance dependent dielectric,
the MD works fine.
However, once I switched to the Generalized Born solvation , using the
same protein topology file used in the distance dependent run in vacuo
above, the simulation failed to run and gave the following message: "bad
atom type: FE".
I used the "check" command in xleap to check the unit "HEM" and found
that although there are 3 "close contacts" between certain "carbon
atoms" overall the unit was "ok".
I do have a total charge of -1.00 for the heme.
Is there some parameter in the input file (e.g. CUT ?) that I have to
experiment with due to the iron? Do I need to change the iron parameters
for GB?
The input file I have used is:
Protein w/ 30.0 GB, constant Volume
&cntrl
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 5000, ntwx = 10000, ntwv = 0, ntwe = 0,
ntwr = -5000,
ntf = 2, ntb = 0,
cut = 30.0, nsnb = 10,
ibelly = 0, ntr = 0,
igb = 1, saltcon = 0.2, gbsa = 1,
imin = 0,
nstlim = 400000,
nscm = 1000,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2,
vlimit = 15.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 2, tol = 0.00001,
lastrst = 8000000,
&end
END
I would appreciate any assistance anyone could offer.
Thanks, Steve
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jan 20 2004 - 15:53:01 PST
