Hi everybody,
I got some problems simulating a molecule containing a sulfonic acid
substitution. The simulation aborts during the pre-processing heat-up
giving no error in the heat.out (it writes the first line of the heat-up
process (NSTEP= 0 TIME (PS) = 0.000 etc.) in section 4.results in the
heat.out).
Input:
heat
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ntr=1,
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
BlAH
2.0
RES 1 357
END
END
The minimization prior to the heating-process worked fine. So I thought
it might be some atomtype issue but antechamber worked fine too
(atomtype sy for the sulfur, o for the double-bonded oxygen and oh for
the hydroxy) and acdoctor only got this warning
Warning: the number of bonded atoms (4) for atom (ID: 20, Name: S20)
does not match
the desired connectivity (2) based on the atom type (S.3)
defined in CORR_NAME_TYPE.DAT.
which acdoctor told me I can ignore too. Leap worked fine too the
resulting molecule/complex got no "strange" bonds/angles etc. I'm doing
the heating-process/equilibration/md-simulation etc. on a GPU cluster
but I don't know if this is the reason why the heating aborts. Maybe
some of you might have experience with that.
Thanks in advance,
Bernhard
--
Bernhard Poll
Institut für Pharmazie
Bundesstr. 45
D 20146 Hamburg | Raum 112
Germany
Tel: +49 (0)40 42838-3626
mail: poll.chemie.uni-hamburg.de
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Received on Mon Dec 10 2012 - 03:00:09 PST
