AMBER Archive (2009)

Subject: Re: [AMBER] Problems in the result of MM_PBSA

From: Sean Zhao (sean.r.zhao_at_gmail.com)
Date: Sun May 10 2009 - 03:23:19 CDT

Ray and David,

Thank you for your suggestion! Now I have performed the sander calculation
for one snapshot. Unfortunately, the problem remains. The energy terms are
still very large.
The output information is shown below:

# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -2568.01 20.16 -3539.41 88.24
201.19 3.75
VDW -549.98 10.38 10037576.86 16855.21 840986.17
1682.59
INT 3462.34 34.63 10459564.23 135701.51 306858.82
24407.73
GAS 344.35 34.49 20493601.68 138682.83 1148046.19
25350.92
PBSUR 75.68 0.53 79.32 0.70
4.10 0.05
PBCAL -1880.09 19.57 -4181.49 482.54
-281.99 6.66
PBSOL -1804.41 19.40 -4102.17 482.22
-277.89 6.62
PBELE -4448.10 16.65 -7720.90 499.67
-80.80 4.34
PBTOT -1460.06 39.05 20489499.51 138726.29 1147768.29
25345.07
GBSUR 77.00 0.55 65.34 0.60
1.86 0.01
GB -1912.17 17.04 -2889.38 43.43
-327.48 6.77
GBSOL -1835.18 17.03 -2824.04 43.32
-325.62 6.76
GBELE -4480.18 15.51 -6428.79 74.20
-126.29 4.54
GBTOT -1490.83 35.95 20490777.64 138691.77 1147720.56
25344.63

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 770.21 98.58
VDW -10879113.02 16738.56
INT -10762960.71 146606.45
GAS -21641303.51 150280.91
PBSUR -7.75 0.39
PBCAL 2583.40 481.43
PBSOL 2575.65 481.29
PBELE 3353.61 501.62
PBTOT -21638727.87 150314.86
GBSUR 9.80 0.25
GB 1304.68 35.06
GBSOL 1314.48 35.02
GBELE 2074.89 86.59
GBTOT -21639989.03 150287.34

2009/5/10 Ray Luo <ray.luo_at_uci.edu>

> Sean,
>
> As Dave suggested, can you run sander manually for one snapshot? Do you see
> similar large internal energy terms? Please show us at least the energy
> section of the output file.
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf
> Of Sean Zhao
> Sent: Friday, May 08, 2009 8:44 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problems in the result of MM_PBSA
>
> Dear Ray and David,
>
> I really appreciate your help! Thank you!
> I have visulized the snapshots via VMD，but nothing abnormal was found. The
> receptor doesn't have structural clash. The complex ( receptor and ligand )
> also didn't run out of the water box. However, there must be something
> wrong
> with my receptor. Now I wonder whether the program Amber can calculate a
> receptor which is a tetramer? My receptor is a homotetramer including four
> helices. The helices are bounded together with the non-bonded interaction.
>
> On Fri, May 8, 2009 at 8:45 PM, David A. Case
> <case_at_biomaps.rutgers.edu>wrote:
>
> > On Fri, May 08, 2009, Sean Zhao wrote:
> >
> > > I used Amber 9 to simulate a small molecule bound in a protein. After I
> > have
> > > finished the MM_PBSA, I found the result ( shown below ) was very
> > > unreasonable. For instance, the delta VDW, INT, GAS, PBTOT and GBTOT
> are
> > all
> > > beyond 10 million. However, no error was reported in the terminal when
> I
> > was
> > > running the MM_PBSA. How can I fix this issue? Any response will be
> > > appreciated.
> >
> > > # COMPLEX RECEPTOR
> > LIGAND
> > > VDW -550.98 22.86 10037286.88 13997.12 840507.41
> > > INT 3434.99 36.17 10647284.69 171501.99 369629.85
> >
> > Note that you have completely unreasonably van der Waals and internal
> > energies for the receptor. Something has gone very badly wrong with that
> > part of the simulation, and you need to find out what it is. Certainly,
> > visual examination is an absolute must here, as Ray pointed out. It has
> > nothing to do with some small difference between am1-bcc and RESP
> charges.
> >
> > In general: the MM-PBSA scripts are intended to be a bookkeeping aid for
> > experienced users, who have well-behaved systems. Everyone should carry
> > out
> > their first such simlations "by hand", doing each step themselves and
> > making
> > sure they understand what is going on. Even for experienced users, the
> > scripts are weak in catching errors -- everyone who has problems needs to
> > have
> > (or develop) the ability to critically examine simulations to look for
> > problems.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> La vie.
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-- 
La vie.
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