AMBER Archive (2008)

Subject: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating

From: xiaonan zhang (
Date: Tue Jun 10 2008 - 07:24:02 CDT

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
 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)
  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 =
 Etot = -121172.0333 EKtot = 782.0864 EPtot =
 BOND = 456.6235 ANGLE = 1821.7021 DIHED =
 1-4 NB = 2425.8535 1-4 EEL = 27446.1028 VDWAALS =
 EELEC = -166641.7581 EHBOND = 0.0000 RESTRAINT =
 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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