Dear All
My name is Xiaonan Zhang, from Shanghai public health clinical
center, PR China. I am a rookie in the AMBER community.
Recently after reading the tutorials, I tried to make my own molecular
dynamics but a serious problem occured which could not
easily be tackled by myself.
Briefly, I am doing MD (with AMBER9, Redhat linux enterprise 4 on a
normal Intel P4 computer) with a protein complex. This
complex has no unusal residues, I just neutrilized the system with sodium
and solvated with solvateoct command, xleap did not
give any errors in molcule prepration except some warnings:
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
**** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
...(several other warnings omitted)
...
...
...
...
total 2182 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CALA 1
CLEU 1
NGLY 1
NPRO 1
WAT 15862
)
(no restraints)
> quit
Then I start minimization, everything is OK. But when I just start heating
process and visulized the trajectory
with VMD. I found something very strange. i.e., The two N terminal nitrogens
were far away from
the original place and caused incredibly long N-H and N-C bonds. I revised
the input parameter to very slow
heating but the output is still the same.Here is the input file I used
(notice the very short time and very low termperature)
&cntrl
imin = 0, ntb = 1,
irest=0, ntx=1
ntpr = 10, ntwx = 10,
ntt = 3, gamma_ln = 1.0,
tempi = 0, temp0 = 30.0,
nstlim = 200, dt = 0.001,
cut = 9,
ntf=2, ntc=2
/
Here is the output.
The temperature rise to 8.87 in just 10 steps!!!
NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 8.87 PRESS =
0.0
Etot = -121172.0333 EKtot = 782.0864 EPtot =
-121954.1197
BOND = 456.6235 ANGLE = 1821.7021 DIHED =
6297.9655
1-4 NB = 2425.8535 1-4 EEL = 27446.1028 VDWAALS =
6239.3910
EELEC = -166641.7581 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2289E-04
------------------------------------------------------------------------------
I really have no idea why this happened.
Could anybody tell me the pitfall that I have walked in ??
That will be greatly appreciated!
Thank you !
Best regards!
Xiaonan Zhang
Research Unit, shanghai public health clinical center
Shanghai ,China
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Received on Wed Jun 11 2008 - 06:07:45 PDT
