Two questions:
1) What does your mdin file look like?
2) What version of sander are you using?
I can't reproduce this with AMBER14. I copied your tleap script verbatim
and used the following mdin:
snglpnt
&cntrl
nstlim = 0, igb = 6
/
The result is as expected:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EGB = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
Did you turn on PBCs somehow?
Regards,
Brian
On Mon, Apr 14, 2014 at 10:59 AM, 黄 <wwsshhjjff00.163.com> wrote:
> Dear Amber Users:
> I know a single water molecule shouldn't have the nonbond interactions.
> I am surprised to see sander will calculates the electrostatic for a single
> TIP3P water molecule simply if the bond between hydrogen atoms is removed.
> What I did is as follows:
> --------- In Leap ----------------------------------------------------
> source leaprc.ff99SB
> w=copy WAT
> deletebond w.1.H1 w.1.H2
> saveamberparm w w.top w.crd
> ---------------------------------------------------------------------
>
>
> The sander output is as follows:
>
> ---------------------------------------------------------------------------------------------
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 3.8140E+01 1.1876E+01 1.9923E+01 H2 3
>
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 0.0000 EEL = 38.1400 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------------------------------
> The electrostatic energy for single water molecule with H-H bond removed
> is 38kcal/mol !
>
>
> Am I doing something wrong? Any help is highly appreciated!
>
>
> Jinfeng
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Apr 14 2014 - 08:30:03 PDT
