Dear All,
I tried to reproduce article data Simonson et al
JACS v126 y2006 pp4167-4180
(Table 1 in the article, right 'AMBER' column and column 'model')
as encouraged in
http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm
Did not get it quite right:
Table 1 in the article,
right 'AMBER' column and column 'model' (in kcal/mol):
Article data MyData(583WAT, OCT9) MyData(1054WAT, OCT12)
dG/dl, l=0 not given 2.6 5.6
dG/dl, l=0.1127 -1.3 -13.9 -13.9
dG/dl, l=0.5 -75.3 -71.7 -71.7
My set up should have the same charges as in the article.
The box is generated by the following tleap input:
logfile logfil
source leaprc.ff99
x=loadpdb asph_model.pdb
solvateOct x TIP3PBOX 9 (or solvateOct x TIP3PBOX 12)
check x
saveamberparm x prmtop prmcrd
quit
This resulted 583 or 1054 additional water molecules
My input file (copied mostly from the tutorial, adapted for explicit
solvent):
model_step2.mdin
model ASH to ASP for pKa calculation
&cntrl
nstlim =3000000, nscm=2000,
ntx=5, irest=1, ntpr=1000,
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
cut=9.0,
dt=0.001,
ntc=2, ntf=2,
ntwr = 10000, ntwx=1000, ntave=1000
icfe=1, clambda=0.11270,
/
Could someone point out my mistake? The force fields differ (in article
parm94 now parm99) but that should not make this big difference. Also the
thermostates are different but neither this should matter much. Also
changing ntc=1 ntf=1 had a minor effect to result.
terveisin, Markus
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Received on Fri Apr 18 2008 - 21:15:29 PDT
