AMBER Archive (2009)

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

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon May 11 2009 - 12:55:12 CDT

Sean,

Please DO NOT use the mmpbsa script, but run sander directly as in the Amber
tutorial. Let us see your output file directly from sander.

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: Sunday, May 10, 2009 1:23 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problems in the result of MM_PBSA

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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>
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> 

--
La vie.
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