I looked in VMD and there is no steric clash. Attached is the prmtop file and restart file.
I have tried both amber 11 and amber 12 = same problem.
I am still trying to set igb=0 as suggested by Dave, but it seems then I'll need ntb=1, and I'll have to solvate the box in leap. Is that right?
Thanks!
Enghui
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Tuesday, December 04, 2012 3:35 PM
To: AMBER Mailing List
Subject: Re: [AMBER] EGB discrepancy between sander and pmemd
If you visualize the structure, does anything look weird?
Also, what version of Amber are you using here? And can you send your
prmtop and inpcrd file so we can reproduce this?
All the best,
Jason
On Tue, Dec 4, 2012 at 11:02 AM, Eng H Yap <eyap.einstein.yu.edu> wrote:
>
> I am trying to minimize a coordinate file and it blowup in PMEMD. when
> examined, EGB = nan when using PMEMD and EGB = -1828.4570 in SANDER. What
> could be the reason?
>
> see below fInput file and results.
>
> Thanks for any advice!
>
> Enghui
>
> my input file :
> minimization 01 - implicit solvent
> &cntrl
> imin = 1, maxcyc = 50,
> ntx = 1, ntc = 1, ntf = 1,
> ntb = 0, ntp = 0,
> ntwx = 10, ntwe = 0, ntpr = 10,
> igb = 1,
> /
>
> PMEMD results:
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 0.0000E+00 N 1
>
> BOND = 9365.8064 ANGLE = 1203.6728 DIHED =
> 1133.0314
> VDWAALS = 4012580.8751 EEL = -7333.4719 EGB =
> NaN
> 1-4 VDW = 13990.5203 1-4 EEL = 4996.2922 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 NaN NaN 0.0000E+00 N 1
>
> BOND = NaN ANGLE = 217137.6841 DIHED =
> 0.0000
> VDWAALS = NaN EEL = NaN EGB =
> NaN
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> 0.0000
>
>
>
> SANDER results:
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.0341E+06 7.5766E+05 2.4814E+07 HA 408
>
> BOND = 9365.8064 ANGLE = 1203.6728 DIHED =
> 1133.0314
> VDWAALS = 4012580.8751 EEL = -7333.4719 EGB =
> -1828.4570
> 1-4 VDW = 13990.5203 1-4 EEL = 4996.2922 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 1.1663E+06 1.6753E+05 5.7409E+06 HA 408
>
> BOND = 9367.3518 ANGLE = 1206.8970 DIHED =
> 1132.9416
> VDWAALS = 1144923.8061 EEL = -7332.3319 EGB =
> -1828.4583
> 1-4 VDW = 13822.8741 1-4 EEL = 4996.1613 RESTRAINT =
> 0.0000
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 04 2012 - 14:30:01 PST
