Re: [AMBER] Error mmpbsa

From: John S <s.john634.gmail.com>
Date: Sat, 2 Jul 2011 01:15:14 -0400

do you refer to this
pbsa -O -i pbsa.in -o pbsa.out -p prmtop -c snapshot1.x
 I have attached my pbsa.out file and it has this warning message.

PB Warning in epsbnd(): No neighbor found for boundary grids total: 6
 PB warning in pb_miccg(): CG maxitn exceeded!

Thanks



On Fri, Jul 1, 2011 at 10:57 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:

> This is a limitation in the previous mmpbsa perl script. It removes
> all output files by default ... do you know how to run sander or pbsa
> by hand? They have the same syntax.
>
> Ray
>
> On Fri, Jul 1, 2011 at 7:21 AM, John S <s.john634.gmail.com> wrote:
> > This is my pbsa.in file , pbsa_com.1.out does not exist
> >
> > &cntrl
> > ntf = 1, ntb = 0,
> > igb = 10, dielc = 1.0,
> > cut = 999.0, nsnb = 99999,
> > scnb = 2.0, scee = 1.2,
> > imin = 1, maxcyc = 0, ntmin = 2,
> > &end
> > &pb
> > epsin = 1.0, epsout = 80.0,
> > istrng = 0, radiopt = 0,
> > sprob = 1.4, space = 0.5,
> > maxitn = 1000, npopt = 1,
> > cavity_surften = 0.0072, cavity_offset = 0.00,
> > npbverb= 1
> > &end
> >
> >
> > On Fri, Jul 1, 2011 at 2:00 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> >
> >> File "rec.all.out" seems to be fine, but there are still no PB
> >> energies in file "com.all.out" ... That's why you have the error
> >> messages "Use of uninitialized value in multiplication value (*) at
> >> ..."
> >>
> >> Can you show the new "pbsa_com.1.out" file? Make sure the file is
> >> really new by removing the old ones if there is any.
> >>
> >> All the best,
> >> Ray
> >>
> >> On Thu, Jun 30, 2011 at 9:17 PM, John S <s.john634.gmail.com> wrote:
> >> > Now I placed the topology files of the receptor , ligand and complex
> in
> >> the
> >> > same directory.
> >> >
> >> > Use of uninitialized value in multiplication (*) at
> >> > /usr/local/apps/amber9/src/m
> >> > m_pbsa/mm_pbsa_statistics.pm line 1336.
> >> > Use of uninitialized value in multiplication (*) at
> >> > /usr/local/apps/amber9/src/m
> >> > m_pbsa/mm_pbsa_statistics.pm line 1336.
> >> > Use of uninitialized value in multiplication (*) at
> >> > /usr/local/apps/amber9/src/m
> >> > m_pbsa/mm_pbsa_statistics.pm line 1336.
> >> > Use of uninitialized value in multiplication (*) at
> >> > /usr/local/apps/amber9/src/m
> >> > m_pbsa/mm_pbsa_statistics.pm line 1336.
> >> > No data for 0+0 PB PB 0
> >> >
> >> > rec.all.out file
> >> >
> >> > MM
> >> > GB
> >> > PB
> >> > MS
> >> > 1
> >> > BOND = 21.4902 ANGLE = 196.1867 DIHED =
> >> > 33.4947
> >> > VDWAALS = 26.0792 EEL = 33.8852 EGB =
> >> > -16.2949
> >> > 1-4 VDW = 62.7277 1-4 EEL = -37.1338 RESTRAINT =
> >> > 0.0000
> >> > surface area = 3992.1336
> >> > corrected reaction field energy: -57.625533
> >> > ECAVITY = 40.8084 EDISPER = 0.0000
> >> > 2
> >> > BOND = 19.5876 ANGLE = 194.4075 DIHED =
> >> > 32.5736
> >> > VDWAALS = 27.9853 EEL = 33.9554 EGB =
> >> > -16.2308
> >> > 1-4 VDW = 64.1462 1-4 EEL = -37.2666 RESTRAINT =
> >> > 0.0000
> >> > surface area = 3986.0617
> >> > corrected reaction field energy: -57.698336
> >> > ECAVITY = 40.8005 EDISPER = 0.0000
> >> >
> >> >
> >> > com.all.out
> >> >
> >> > MM
> >> > GB
> >> > PB
> >> > MS
> >> > 1
> >> > BOND = 27.1075 ANGLE = 525.9645 DIHED =
> >> > 565.9391
> >> > VDWAALS = -25.4483 EEL = 0.0000 EGB =
> >> > 0.0000
> >> > 1-4 VDW = 137.9756 1-4 EEL = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > surface area = 4322.1199
> >> > ECAVITY = 45.0125 EDISPER = 0.0000
> >> > 2
> >> > BOND = 24.6461 ANGLE = 524.6252 DIHED =
> >> > 564.9438
> >> > VDWAALS = -24.3942 EEL = 0.0000 EGB =
> >> > 0.0000
> >> > 1-4 VDW = 139.8923 1-4 EEL = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > surface area = 4313.5184
> >> > ECAVITY = 44.9180 EDISPER = 0.0000
> >> >
> >> > MM
> >> > GB
> >> > PB
> >> > MS
> >> > 1
> >> > BOND = 5.6172 ANGLE = 329.7777 DIHED =
> >> > 532.4443
> >> > VDWAALS = -41.6611 EEL = 0.0000 EGB =
> >> > 0.0000
> >> > 1-4 VDW = 75.2478 1-4 EEL = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > surface area = 407.1399
> >> > ECAVITY = 5.9205 EDISPER = 0.0000
> >> > 2
> >> > BOND = 5.0585 ANGLE = 330.2177 DIHED =
> >> > 532.3702
> >> > VDWAALS = -41.8098 EEL = 0.0000 EGB =
> >> > 0.0000
> >> > 1-4 VDW = 75.7461 1-4 EEL = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > surface area = 411.7751
> >> > ECAVITY = 5.8871 EDISPER = 0.0000
> >> >
> >> >
> >> > On Mon, Jun 27, 2011 at 11:01 PM, Bill Miller III <
> brmilleriii.gmail.com
> >> >wrote:
> >> >
> >> >> The Unit 8 Error message means that pbsa cannot find your prmtop file
> >> that
> >> >> you specified. Double check that you have properly defined the
> location
> >> and
> >> >> name of your complex prmtop file in the mm_pbsa.pl input file.
> >> >>
> >> >> -Bill
> >> >>
> >> >> On Mon, Jun 27, 2011 at 10:44 PM, John S <s.john634.gmail.com>
> wrote:
> >> >>
> >> >> > The following is my pbsa_com.1.out file.Is this related to my
> input
> >> >> file,
> >> >> > why does MM=1 work with results on gas phase energies
> >> >> >
> >> >> > -------------------------------------------------------
> >> >> > Amber 9 PBSA Scripps/UCSF 2006
> >> >> > -------------------------------------------------------
> >> >> >
> >> >> > | Run on 06/26/2011 at 23:17:31
> >> >> > [-O]verwriting output
> >> >> >
> >> >> > File Assignments:
> >> >> > | MDIN: pbsa.in
> >> >> >
> >> >> > | MDOUT:
> >> >> > p4g_com.1.out
> >> >> > |INPCRD: ./p4g_com.crd.1
> >> >> > | PARM: /p4
> >> >> > |RESTRT:
> >> >> > restrt
> >> >> > | REFC:
> >> >> > refc
> >> >> > | MDVEL:
> >> >> > mdvel
> >> >> > | MDEN:
> >> >> > mden
> >> >> > | MDCRD:
> >> >> > mdcrd
> >> >> > |MDINFO:
> >> >> > mdinfo
> >> >> > |INPDIP:
> >> >> > inpdip
> >> >> > |RSTDIP:
> >> >> > rstdip
> >> >> >
> >> >> >
> >> >> > Here is the input file:
> >> >> >
> >> >> > File generated by mm_pbsa.pl. Using
> >> >> > PB
> >> >> > &cntrl
> >> >> >
> >> >> > ntf = 1, ntb =
> >> >> > 0,
> >> >> > igb = 10, dielc =
> >> >> > 1.0,
> >> >> > cut = 999.0, nsnb =
> >> >> > 99999,
> >> >> > scnb = 2.0, scee =
> >> >> > 1.2,
> >> >> > imin = 1, maxcyc = 0, ntmin =
> >> >> > 2,
> >> >> > &end
> >> >> >
> >> >> > &pb
> >> >> >
> >> >> > epsin = 1.0, epsout =
> >> >> > 80.0,
> >> >> > istrng = 0, radiopt =
> >> >> > 0,
> >> >> > sprob = 1.4, space =
> >> >> > 0.5,
> >> >> > maxitn = 1000, npopt =
> >> >> > 1,
> >> >> > cavity_surften = 0.0072, cavity_offset =
> >> >> > 0.00,
> >> >> > npbverb=
> >> >> > 1
> >> >> > &end
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >>
> --------------------------------------------------------------------------------
> >> >> > 1. RESOURCE USE:
> >> >> >
> >> >> >
> >> >>
> >>
> --------------------------------------------------------------------------------
> >> >> >
> >> >> > |
> >> >> > Flags:
> >> >> >
> >> >> >
> >> >> > Unit 8 Error on OPEN: /p4g/
> >> >> >
> >> >> >
> >> >> > On Mon, Jun 27, 2011 at 6:41 AM, Bill Miller III <
> >> brmilleriii.gmail.com
> >> >> > >wrote:
> >> >> >
> >> >> > > What error message is in the pbsa output files: pbsa_com.1.out ?
> >> That
> >> >> > > should
> >> >> > > be where a more message is present.
> >> >> > >
> >> >> > > -Bill
> >> >> > >
> >> >> > > On Sun, Jun 26, 2011 at 11:29 PM, John S <s.john634.gmail.com>
> >> wrote:
> >> >> > >
> >> >> > > > Dear Amber users,
> >> >> > > > I am using Amber 9 for mmpbsa calculations (mm_pbsa.pl ), for
> MM
> >> =1,
> >> >> > I
> >> >> > > > get
> >> >> > > > no errors whereas when I use PB=1 MM=1 , it gives the following
> >> error
> >> >> > .Is
> >> >> > > > this related to my input files or something to do with the
> >> >> > installation
> >> >> > > > .Please let me know
> >> >> > > >
> >> >> > > > Unit 8 Error on OPEN: /p4g/
> >> >> > > > /usr/local/apps/amber9/exe/pbsa -O -i pbsa.in -o
> >> >> pbsa_com.1.out
> >> >> > > -c
> >> >> > > > ./p4g_com.crd.1 -p /prep/p4g.prmtop not successful
> >> >> > > >
> >> >> > > >
> >> >> > > > my pbsa.in file is as below
> >> >> > > >
> >> >> > > > &cntrl
> >> >> > > > ntf = 1, ntb = 0,
> >> >> > > > igb = 10, dielc = 1.0,
> >> >> > > > cut = 999.0, nsnb = 99999,
> >> >> > > > scnb = 2.0, scee = 1.2,
> >> >> > > > imin = 1, maxcyc = 0, ntmin = 2,
> >> >> > > > &end
> >> >> > > > &pb
> >> >> > > > epsin = 1.0, epsout = 80.0,
> >> >> > > > istrng = 0, radiopt = 0,
> >> >> > > > sprob = 1.4, space = 0.5,
> >> >> > > > maxitn = 1000, npopt = 1,
> >> >> > > > cavity_surften = 0.0072, cavity_offset = 0.00,
> >> >> > > > npbverb= 1
> >> >> > > > &end
> >> >> > > >
> >> >> > > > p4g_com.all.out
> >> >> > > >
> >> >> > > > MM
> >> >> > > > GB
> >> >> > > > PB
> >> >> > > > MS
> >> >> > > > 1
> >> >> > > > BOND = 27.1075 ANGLE = 525.9645 DIHED =
> >> >> > > > 565.9391
> >> >> > > > VDWAALS = -25.4483 EEL = 0.0000 EGB =
> >> >> > > > 0.0000
> >> >> > > > 1-4 VDW = 137.9756 1-4 EEL = 0.0000 RESTRAINT =
> >> >> > > > 0.0000
> >> >> > > > surface area = 4322.1199
> >> >> > > >
> >> >> > > > Thanks
> >> >> > > > John
> >> >> > > > _______________________________________________
> >> >> > > > AMBER mailing list
> >> >> > > > AMBER.ambermd.org
> >> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> > > >
> >> >> > >
> >> >> > >
> >> >> > >
> >> >> > > --
> >> >> > > Bill Miller III
> >> >> > > Quantum Theory Project,
> >> >> > > University of Florida
> >> >> > > Ph.D. Graduate Student
> >> >> > > 352-392-6715
> >> >> > > _______________________________________________
> >> >> > > AMBER mailing list
> >> >> > > AMBER.ambermd.org
> >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> > >
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Bill Miller III
> >> >> Quantum Theory Project,
> >> >> University of Florida
> >> >> Ph.D. Graduate Student
> >> >> 352-392-6715
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Fri Jul 01 2011 - 22:30:06 PDT
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