AMBER Archive (2008)

Subject: AMBER: reproducing with explicit water

From: Markus Kaukonen (
Date: Mon Mar 31 2008 - 01:34:48 CDT

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

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

This resulted 583 or 1054 additional water molecules

My input file (copied mostly from the tutorial, adapted for explicit

model ASH to ASP for pKa calculation
  nstlim =3000000, nscm=2000,
  ntx=5, irest=1, ntpr=1000,
  tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
  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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