dear Francois,
Many many thanks for your valuable suggestions.
On Thu, Oct 31, 2013 at 12:30 AM, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Sander error (Concha, Monica)
> 2. Re: Sander error (Jason Swails)
> 3. calculatie the energy between two groups of atoms from an MD
> trajectory, is it possible? (Jose Borreguero)
> 4. Re: Sander error (Concha, Monica)
> 5. Re: Sander error (Jason Swails)
> 6. Re: calculatie the energy between two groups of atoms from an
> MD trajectory, is it possible? (Brian Radak)
> 7. Re: Soft-core questions for TI method (Ying-Chieh Sun)
> 8. Installation error (Dhananjay)
> 9. Re: Trajectory determination and directionality in TI with
> softcore potentials (Ying-Chieh Sun)
> 10. Free binding energy calculations for Zinc dependent ligands
> (Tivani Mashamba)
> 11. Amber 12 Updater error on Arch linux (M. Reza Ganjalikhany)
> 12. Re: Amber 12 Updater error on Arch linux (Jason Swails)
> 13. Re: Installation error (Jason Swails)
> 14. Re: Installation error (David A Case)
> 15. Re: problem after minimization of pure DMF (FyD)
> 16. Re: Free binding energy calculations for Zinc dependent
> ligands (Jason Swails)
> 17. Re: calculatie the energy between two groups of atoms from an
> MD trajectory, is it possible? (Jose Borreguero)
> 18. Re: about rms atomic fluctuation for protein crystal .thank
> you very much! (Pawel)
> 19. Re: optimization using gaussian and RESP using antechamber
> (Tanmoy Paul)
> 20. Hbond analysis (Fabr?cio Bracht)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Oct 2013 20:09:24 +0000
> From: "Concha, Monica" <Monica.Concha.ARS.USDA.GOV>
> Subject: [AMBER] Sander error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> D8D4E9792FFEE24E9B4CEDE41D51E2E8103BD5.001FSN2MPN1-023.001f.mgd2.msft.net>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I recently installed AmberTools13 for the first time. However,
> when I try to
> run sander I find that it is not in the amber12/bin folder and I get the
> error message that amber12/bin/sander does not exist. Does anyone know
> what am I doing wrong?
>
> error message when I run sander:
> $AMBERHOME/bin/sander -O -i polyAT_vac.in -o polyAT_vac.out -c
> polyAT_vac.inpcrd -p polyAT_vac.prmtop -r polyAT_vac.rst
> -bash: /home/mconcha/amber12/bin/sander: No such file or directory
>
> This is how I set my environment:
> export AMBERHOME=/home/mconcha/amber12
> export
> PATH=$PATH:/home/mconcha/amber12/bin:/home/glenn/amber10_distribution/amber10/bin
>
> AmberTools 13 is in /home/mconcha/amber12/ambertools13
> Amber10 is in /home/glenn/amber10_distribution/amber10
>
> Thanks,
>
> Monica C. Concha
> Physical Science Technician
> Cotton Structure and Quality Research
> Southern Regional Research Center
> 1100 Robert E. Lee Blvd.
> New Orleans, LA 70124
> monica.concha.ars.usda.gov
> phone: 504-286-4252
>
>
>
>
>
> This electronic message contains information generated by the USDA solely
> for the intended recipients. Any unauthorized interception of this message
> or the use or disclosure of the information it contains may violate the law
> and subject the violator to civil or criminal penalties. If you believe you
> have received this message in error, please notify the sender and delete
> the email immediately.
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 29 Oct 2013 16:19:41 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Sander error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rJ+m2CtxVZW0PHBk8yqjmjF4q+TtcLZ8=E+Ph=
> DUDYTw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Oct 29, 2013 at 4:09 PM, Concha, Monica
> <Monica.Concha.ars.usda.gov>wrote:
>
> > Hi,
> >
> > I recently installed AmberTools13 for the first time. However,
> > when I try to
> > run sander I find that it is not in the amber12/bin folder and I get the
> > error message that amber12/bin/sander does not exist. Does anyone know
> > what am I doing wrong?
> >
>
> sander is part of Amber 12. If you do not have an Amber 12 license then
> sander 12 will not be built.
>
> As you mentioned, you do have Amber 10, so you will need to use sander from
> /home/glenn/amber10_distribution/amber10/bin instead.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 29 Oct 2013 16:37:07 -0400
> From: Jose Borreguero <borreguero.gmail.com>
> Subject: [AMBER] calculatie the energy between two groups of atoms
> from an MD trajectory, is it possible?
> To: amber mailing list <amber.ambermd.org>
> Message-ID:
> <CAEee4gUQuTc5twEWAwcAg8csZjbEvAvutut=
> tGDNpiQouGpwCg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber users,
>
> I was wondering whether it is possible to read and MD trajectory and
> calculate the energy between two groups of atoms, for instance, between two
> nearby amino acids. From the manual, it seems that imin=5 will read the
> trajectory and output the energy of the whole system. Can one select the
> atoms for which Amber should calculate the energy?
>
> -Jose
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 29 Oct 2013 20:39:09 +0000
> From: "Concha, Monica" <Monica.Concha.ARS.USDA.GOV>
> Subject: Re: [AMBER] Sander error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> D8D4E9792FFEE24E9B4CEDE41D51E2E8103BFF.001FSN2MPN1-023.001f.mgd2.msft.net>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Jason M. Swails,
> Thank you for your quick answer!
> How do I accomplish that?
> Thanks again!
>
>
> Monica C. Concha
> Physical Science Technician
> Cotton Structure and Quality Research
> Southern Regional Research Center
> 1100 Robert E. Lee Blvd.
> New Orleans, LA 70124
> monica.concha.ars.usda.gov
> phone: 504-286-4252
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Tuesday, October 29, 2013 3:20 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Sander error
>
> On Tue, Oct 29, 2013 at 4:09 PM, Concha, Monica
> <Monica.Concha.ars.usda.gov>wrote:
>
> > Hi,
> >
> > I recently installed AmberTools13 for the first time. However,
> > when I try to run sander I find that it is not in the amber12/bin
> > folder and I get the error message that amber12/bin/sander does not
> > exist. Does anyone know what am I doing wrong?
> >
>
> sander is part of Amber 12. If you do not have an Amber 12 license then
> sander 12 will not be built.
>
> As you mentioned, you do have Amber 10, so you will need to use sander
> from /home/glenn/amber10_distribution/amber10/bin instead.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> This electronic message contains information generated by the USDA solely
> for the intended recipients. Any unauthorized interception of this message
> or the use or disclosure of the information it contains may violate the law
> and subject the violator to civil or criminal penalties. If you believe you
> have received this message in error, please notify the sender and delete
> the email immediately.
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 Oct 2013 16:55:36 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Sander error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rUWcmTuDWO+z_79iOrNSP046D31XpE=
> BUdv-nAKBWqPw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Oct 29, 2013 at 4:39 PM, Concha, Monica
> <Monica.Concha.ars.usda.gov>wrote:
>
> > Jason M. Swails,
> > Thank you for your quick answer!
> > How do I accomplish that?
> >
>
> Well since you already added that directory to your path, just use "sander"
> instead of $AMBERHOME/bin/sander.
>
>
> > Thanks again!
> >
> >
> > Monica C. Concha
> > Physical Science Technician
> > Cotton Structure and Quality Research
> > Southern Regional Research Center
> > 1100 Robert E. Lee Blvd.
> > New Orleans, LA 70124
> > monica.concha.ars.usda.gov
> > phone: 504-286-4252
> >
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: Tuesday, October 29, 2013 3:20 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Sander error
> >
> > On Tue, Oct 29, 2013 at 4:09 PM, Concha, Monica
> > <Monica.Concha.ars.usda.gov>wrote:
> >
> > > Hi,
> > >
> > > I recently installed AmberTools13 for the first time. However,
> > > when I try to run sander I find that it is not in the amber12/bin
> > > folder and I get the error message that amber12/bin/sander does not
> > > exist. Does anyone know what am I doing wrong?
> > >
> >
> > sander is part of Amber 12. If you do not have an Amber 12 license then
> > sander 12 will not be built.
> >
> > As you mentioned, you do have Amber 10, so you will need to use sander
> > from /home/glenn/amber10_distribution/amber10/bin instead.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> >
> > This electronic message contains information generated by the USDA solely
> > for the intended recipients. Any unauthorized interception of this
> message
> > or the use or disclosure of the information it contains may violate the
> law
> > and subject the violator to civil or criminal penalties. If you believe
> you
> > have received this message in error, please notify the sender and delete
> > the email immediately.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 29 Oct 2013 17:24:52 -0400
> From: Brian Radak <radak004.umn.edu>
> Subject: Re: [AMBER] calculatie the energy between two groups of atoms
> from an MD trajectory, is it possible?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAJrka9wPP1p29FYR-+YJtWLgor+2a+RwJvhL6TyF9xrqn1+dew.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Three methods come to mind:
>
> 1) use cpptraj to strip out all but the atoms you want
>
> 2) use parmed to make a new prmtop with the only the interactions you want
>
> 3) if the energy is only a function of a few distances, extract those and
> recompute it by hand
>
> All of those energies will likely be slightly different if you are using
> PME, since then the energy isn't strictly pairwise in the reciprocal sum.
>
> Regards,
> Brian
>
>
> On Tue, Oct 29, 2013 at 4:37 PM, Jose Borreguero <borreguero.gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I was wondering whether it is possible to read and MD trajectory and
> > calculate the energy between two groups of atoms, for instance, between
> two
> > nearby amino acids. From the manual, it seems that imin=5 will read the
> > trajectory and output the energy of the whole system. Can one select the
> > atoms for which Amber should calculate the energy?
> >
> > -Jose
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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.
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 30 Oct 2013 16:31:57 +0800
> From: "Ying-Chieh Sun" <sun.ntnu.edu.tw>
> Subject: Re: [AMBER] Soft-core questions for TI method
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <005c01ced54a$7f5a65d0$7e0f3170$.ntnu.edu.tw>
> Content-Type: text/plain; charset="us-ascii"
>
> I recalled the tolerance of difference in coordinates of common atoms is
> 0.001 A. A good practice is to generate child coordinate file by copying
> parent file, and then modify the copied file. Hope this help. Ying-chieh
> Sun
>
> -----Original Message-----
> From: yuandandan [mailto:yuandandan06.outlook.com]
> Sent: Monday, October 7, 2013 3:43 PM
> To: amber.ambermd.org
> Subject: [AMBER] Soft-core questions for TI method
>
> Hi,
>
>
>
>
> I encountered a question when I used soft-core for Thermodynamic
> Integration
> calculation.
>
> In fact, I put two molecules into a cage to calculate the relative binding
> energy using TI method. Atoms in blue rectangular box (questions.doc in
> attachment) are the six unique atoms.
>
> This is a VDW process.
> I created files similar to amber tutorial A9. The files seems all right,
> the
> same order and coordinates for common atoms.
> Then, I ran sander. The error is:
>
> Softcore Mask :TWO.C9,H18,H19,C10,O1,O2; matches 6 atoms
> this run corresponds to V0, its softcore atoms interact fully for
> lambda=0
> this process: 9257 atoms, partner process: 9257 atoms
> Checking for mismatched coordinates.
> WARNING: Local coordinate 1246 differs from partner coordinate 1246
> !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 1247 differs from partner coordinate 1247
> !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 1248 differs from partner coordinate 1248
> !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 1249 differs from partner coordinate 1249
> !
> SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate
> disagreement
> Check input files.
>
> I checked the files and found that coordinates 1246,12647,1248 correspond
> to common atom Carbon.
>
> Also, I found that the output files of minimization (.out) were finished
> normal, however, the coordinates of common atoms didn't keep the same in 0
> and 1 when compare the two output .rst files, and then the equilibrium
> failed.
>
> The attachment file includes all files for the first window calculation.
> Could you please check the file for me and give me any solutions?
> Thank you!
>
> Best,
>
> Dandan yuan, PHD students
> Nanjing University
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 30 Oct 2013 16:41:49 +0800
> From: Dhananjay <dhananjay.c.joshi.gmail.com>
> Subject: [AMBER] Installation error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPxp-0RKO-xVUn2On+84pPc4ps-JGOU5u9rBis4H0Ksfi1sW=
> A.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> I got an error message while installing amber on newly installed Debian
> 7.0.
> The error appeared when I run "make install", as follows:
>
>
> o pb_augdrv.o gmresX.o interpX.o matvec3.o gen_dx_file.o aug_iccg.o
> membrane.o fftw3.o \
> ../lib/nxtsec.o ../lib/random.o -lfftw3 \
> -L/opt/amber12/lib -larpack -llapack -lblas
> /opt/amber12/lib/libfftw3.a(trig.o): In function `cexpl_sincos':
> trig.c:(.text+0x189): undefined reference to `__libm_sse2_sincos'
> /opt/amber12/lib/libfftw3.a(trig.o): In function `fftw_mktriggen':
> trig.c:(.text+0x41e): undefined reference to `__libm_sse2_sincos'
> trig.c:(.text+0x52e): undefined reference to `__libm_sse2_sincos'
> /opt/amber12/lib/libfftw3.a(dht-rader.o): In function `apply':
> dht-rader.c:(.text+0xf9): undefined reference to `_intel_fast_memset'
> /opt/amber12/lib/libfftw3.a(dht-rader.o): In function `awake':
> dht-rader.c:(.text+0x70f): undefined reference to `_intel_fast_memset'
> /opt/amber12/lib/libfftw3.a(rank0.o): In function `apply_memcpy':
> rank0.c:(.text+0x620): undefined reference to `__intel_ssse3_memcpy'
> /opt/amber12/lib/libfftw3.a(rank0.o): In function `apply_memcpy_loop':
> rank0.c:(.text+0x76a): undefined reference to `__intel_ssse3_memcpy'
> /opt/amber12/lib/libfftw3.a(rank0.o): In function `memcpy_loop':
> rank0.c:(.text+0x887): undefined reference to `__intel_ssse3_memcpy'
> /opt/amber12/lib/libfftw3.a(vrank3-transpose.o): In function `apply_gcd':
> vrank3-transpose.c:(.text+0xab): undefined reference to
> `__intel_ssse3_memcpy'
> vrank3-transpose.c:(.text+0x14b): undefined reference to
> `__intel_ssse3_memcpy'
>
> /opt/amber12/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x671):
> more undefined references to `__intel_ssse3_memcpy' follow
> /opt/amber12/lib/libfftw3.a(vrank3-transpose.o): In function
> `apply_toms513':
> vrank3-transpose.c:(.text+0xe9f): undefined reference to
> `_intel_fast_memset'
> vrank3-transpose.c:(.text+0xfaf): undefined reference to
> `__intel_ssse3_memcpy'
> vrank3-transpose.c:(.text+0xfcc): undefined reference to
> `__intel_ssse3_memcpy'
> vrank3-transpose.c:(.text+0x10e0): undefined reference to
> `__intel_ssse3_memcpy'
> vrank3-transpose.c:(.text+0x110a): undefined reference to
> `__intel_ssse3_memcpy'
> vrank3-transpose.c:(.text+0x1246): undefined reference to
> `__intel_ssse3_memcpy'
>
> /opt/amber12/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1261):
> more undefined references to `__intel_ssse3_memcpy' follow
> collect2: error: ld returned 1 exit status
> make[2]: *** [pbsa] Error 1
> make[2]: Leaving directory `/opt/amber12/AmberTools/src/pbsa'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/opt/amber12/AmberTools/src'
> make: *** [install] Error 2
>
>
> Any suggestions please !
>
> Thanking you in advance.
>
>
> -- Joshi
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 30 Oct 2013 16:43:06 +0800
> From: "Ying-Chieh Sun" <sun.ntnu.edu.tw>
> Subject: Re: [AMBER] Trajectory determination and directionality in TI
> with softcore potentials
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <005f01ced54c$0de05700$29a10500$.ntnu.edu.tw>
> Content-Type: text/plain; charset="us-ascii"
>
> My quick comment to your question is ... the 'truncation' in numbers may
> give deviation you mentioned. Therefore, there is tolerance in difference
> of
> calculated <dV/d lambda> statistically. Ying-chieh Sun
>
> -----Original Message-----
> From: Ryan Muraglia [mailto:rmuraglia.gmail.com]
> Sent: Wednesday, September 18, 2013 3:39 AM
> To: amber.ambermd.org
> Subject: [AMBER] Trajectory determination and directionality in TI with
> softcore potentials
>
> Hello,
>
> I am using thermodynamic integration in AMBER 11 with softcore potentials,
> and I am finding curious behavior that I cannot explain by reading the
> manual or tutorials, so I was hoping that this would be an appropriate
> place
> to seek an explanation or a suggestion for additional resources to consult.
>
> I have been trying to compute the free energy difference of the mutation of
> an alanine residue (in an alanine tripeptide, AAA) to a valine residue
> (making the tripeptide AVA) in a box of TIP3P water as a test case. I can
> share my input files if they will help. The masked atoms are the sidechains
> of the residues that are being swapped.
>
> One of my sanity checks was to run the TI scheme "backwards," meaning that
> in the groupfile, I flipped the order of the sander calls. I was expecting
> that the dv/dlambda curves for the forward and backward processes would
> mirror each other (with one taking on negative values). For example I would
> expect that AAA -> AVA for lambda=0.25 would take on the negated value for
> average dv/dl as AVA -> AAA for lambda=0.75, and that the values at
> lambda=0.5 would be exact opposites.
>
> I found that my expectation was not met. I used linear mixing of the
> potentials (klambda=1) and I used the same, default, fixed random seed for
> the Langevin dynamics (ig=71227) for each simulation, so I am not sure
> where
> the deviation from my expected behavior is coming from. As I understand it,
> 0.25 "forward" should be evolving according to the same mixed potential as
> 0.75 "backward." Digging deeper, I found that the trajectories of the two
> processes did not match, which could cause the discrepancy in dv/dlambda
> values down the line.
>
> All of this background is simply to ask, how are the trajectories
> determined
> in TI? There is obviously something more nuanced than simply stating that
> the system evolves according to a mixed potential. Do non-masked atoms
> share
> the same trajectory in the two endpoint states (V0 and V1)? How is
> information from the two processes representing V0 and V1 combined to
> determine atomic positions in the next step? And most importantly, is this
> discrepancy to be expected, and if so, can it be characterized in a
> meaningful manner, or is it a byproduct of the implementation?
>
> Thank you very much for reading. Any insight or suggestions for further
> reading would be greatly appreciated.
>
> --
> Ryan Muraglia
> rmuraglia.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 30 Oct 2013 09:09:05 +0000 (GMT)
> From: Tivani Mashamba <tivanim.yahoo.co.uk>
> Subject: [AMBER] Free binding energy calculations for Zinc dependent
> ligands
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <1383124145.20231.YahooMailNeo.web133201.mail.ir2.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> ?
> Hi
> I am trying to calculate binding free energy for Zinc dependent receptor:
> ligand system, my receptor containd 2 Zinc atoms and the ligands are Zn
> depedent. I have included the 2 Zn atoms in the SUB, see below:
>
> pirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i mmpbsa.in -o
> mmpbsa.dat -sp com_solvated.top -cp com.top -rp rec.top -lp LIG.top -y
> ZN1.top -lp ZN2.top -y md.mdcrd > mmpbsa.log
>
>
> However, I am not getting any result and here is the error message that I
> am getting.
>
> PrmtopError: Complex natom != receptor natom + ligand natom
> Exiting. All files have been retained.
>
> I shall be very grateful if you can assist me on this.
>
> Best wishes
> Tivani
>
>
> ------------------------------
>
> Message: 11
> Date: Wed, 30 Oct 2013 09:52:16 +0000
> From: "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> Subject: [AMBER] Amber 12 Updater error on Arch linux
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CACQTqGWaNN6MLdDiK1pEfyupO3RHsydVsq_ZXzKdiwjfa-2hMA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber Users,
>
> I am trying to compile Amber 12 on Arch linux (latest kernel 3.11.6), but I
> get the error message from the biginig when updater tries to autoupdate
> Amber as below. Also, the rest of check points pass successfully at
> configuration step.
>
> Any help will be greatly appreciated,
>
> [root.localhost amber12]# ./configure gnu
> Checking for updates...
> File "./update_amber", line 30
> except AmberUpdaterError, err:
> ^
> SyntaxError: invalid syntax
> Check for updates failed.
> Searching for python2... Found python2.7: /usr/bin/python2.7
>
> Obtaining the gnu suite version:
> gcc -v
> The version is 4.8.2
>
> Testing the gcc compiler:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c
> gfortran -O0 -c -o testp.f.o testp.f
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> testp.f.o -lgfortran -w
> OK
>
> Testing pointer size:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> test_pointer_size.c
> Detected 64 bit operating system.
>
> Testing flex: OK
>
> Configuring NetCDF (may be time-consuming)...
>
> NetCDF configure succeeded.
>
> Checking for zlib: OK
>
> Checking for libbz2: OK
>
> Configuring fftw-3.3 (may be time-consuming)...
>
> fftw-3.3 configure succeeded.
>
> Configuring XBLAS (may be time-consuming)...
>
> XBLAS configure succeeded.
>
> Configuring MTK++ (may be time-consuming)...
>
> MTK++-0.2.0 configure succeeded.
>
> The configuration file, config.h, was successfully created.
>
> The next step is to type 'make install'
>
> Cleaning the src directories. This may take a few moments.
> Configure complete.
>
>
> ------------------------------
>
> Message: 12
> Date: Wed, 30 Oct 2013 07:20:18 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Amber 12 Updater error on Arch linux
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3q6hLenBJryicPTLk-X+mbOtd-cFTsdj_0QFTUS=
> 1XdZg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Oct 30, 2013 at 5:52 AM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I am trying to compile Amber 12 on Arch linux (latest kernel 3.11.6),
> but I
> > get the error message from the biginig when updater tries to autoupdate
> > Amber as below. Also, the rest of check points pass successfully at
> > configuration step.
> >
> > Any help will be greatly appreciated,
> >
> > [root.localhost amber12]# ./configure gnu
> > Checking for updates...
> > File "./update_amber", line 30
> > except AmberUpdaterError, err:
> > ^
> > SyntaxError: invalid syntax
> >
>
> This is valid syntax for Python 2, but not for Python 3. We are reaching a
> point where newer Linux distributions are starting to finally retire Python
> 2 as their main system Python and they are moving to Python 3. According
> to the Arch Linux Wiki, Python 3 is now the default Python version shipped
> with that Linux distribution. Because Python 2.4 is still a commonly-used
> default Python version on RHEL 5 -- which is still popular for some larger
> clusters -- it was important for update_amber to support Python 2.4 through
> 2.7 (but at the time of writing, no distros had fully switched to Python
> 3). The upcoming AmberTools 14 will feature an update_amber that uses
> syntax fully compatible with both Python 2 (2.4+) and Python 3
> (significantly trickier than it would seem). For the time being, though,
> Python 2 is required for AmberTools 13's updating script.
>
> Long story short, change the shebang line of update_amber from
>
> #!/usr/bin/env python
>
> to
>
> #!/usr/bin/env python2
>
> See the Arch Linux wiki page on Python for more information:
> https://wiki.archlinux.org/index.php/python
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 13
> Date: Wed, 30 Oct 2013 07:43:58 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Installation error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3qD96Bew6ugGr+fhC+UBs66yjNEUK1wNTvyit2KOnxO4w.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Oct 30, 2013 at 4:41 AM, Dhananjay <dhananjay.c.joshi.gmail.com
> >wrote:
>
> > Hello,
> >
> > I got an error message while installing amber on newly installed Debian
> > 7.0.
> > The error appeared when I run "make install", as follows:
> >
> >
> > o pb_augdrv.o gmresX.o interpX.o matvec3.o gen_dx_file.o aug_iccg.o
> > membrane.o fftw3.o \
> > ../lib/nxtsec.o ../lib/random.o -lfftw3 \
> > -L/opt/amber12/lib -larpack -llapack -lblas
> > /opt/amber12/lib/libfftw3.a(trig.o): In function `cexpl_sincos':
> > trig.c:(.text+0x189): undefined reference to `__libm_sse2_sincos'
> > /opt/amber12/lib/libfftw3.a(trig.o): In function `fftw_mktriggen':
> > trig.c:(.text+0x41e): undefined reference to `__libm_sse2_sincos'
> > trig.c:(.text+0x52e): undefined reference to `__libm_sse2_sincos'
> > /opt/amber12/lib/libfftw3.a(dht-rader.o): In function `apply':
> > dht-rader.c:(.text+0xf9): undefined reference to `_intel_fast_memset'
> > [snip]
> >
>
>
>
> > Any suggestions please !
> >
>
> It looks like you are trying to use the Intel compilers, but that you don't
> have the environment for those compilers set up correctly. Intel provides
> sourceable scripts to set up your environment, and I'd suggest you use
> those. Look at the end of this page:
>
> http://software.intel.com/en-us/articles/using-intel-compilers-for-linux-with-ubuntu
>
> An alternative is to switch to the GNU compilers.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 14
> Date: Wed, 30 Oct 2013 07:52:45 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Installation error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20131030115245.GA55796.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Wed, Oct 30, 2013, Dhananjay wrote:
> >
> > I got an error message while installing amber on newly installed Debian
> > 7.0.
>
> What compiler are you using? What arguments did you give to configure?
> Posting your resulting config.h file might help.
>
> Also, had you compiled earlier with and different compiler? (e.g. before
> you
> installed the new OS)? You might try typing "make uninstall" (in
> $AMBERHOME),
> then configuring and compiling again. Use "gnu" as the compiler suite if
> you
> are not already doing that (or even if you are!)
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 30 Oct 2013 12:59:20 +0100
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] problem after minimization of pure DMF
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: Piotr Cieplak <pcieplak.sanfordburnham.org>,
> fan.wang.u-picardie.fr
> Message-ID: <20131030125920.fy0oqlkn6o08cg4k.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Sohag Biswas,
>
> We just generated a force field for DMF - we had to correct a bug in
> our dictionary of atom types for the aldehyde organic function.
>
> The job took ~110 seconds on a laptop with 4 cores.
>
> See http://q4md-forcefieldtools.org/Help/DMF/ &
> http://q4md-forcefieldtools.org/Help/DMF/Configuration.py
>
> The resp inputs:
>
> http://q4md-forcefieldtools.org/Help/DMF/Data-R.E.D.Server/Mol_m1/input1-sm_m1.in
>
> http://q4md-forcefieldtools.org/Help/DMF/Data-R.E.D.Server/Mol_m1/input2-sm_m1.in
>
> The FF library:
>
> http://q4md-forcefieldtools.org/Help/DMF/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2
>
> The frcmod file:
>
> http://q4md-forcefieldtools.org/Help/DMF/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
>
> The leaprc file:
>
> http://q4md-forcefieldtools.org/Help/DMF/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft
>
> regards, Francois
>
>
> > I'm trying to minimize the initial structure 50 DMF. After minimization,
> i
> > can see that my methyl hydrogens of DMF are making bond. how can i solve
> > this problem. someone please help me. Here i'm giving my frcmod file and
> > min.in input. Thank you.
> >
> > remark goes here
> > MASS
> > o 16.0 0.000
> > c 12.0 0.000
> > h5 1.0 0.000
> > n 14.0 0.000
> > c3 12.0 0.000
> > h1 1.0 0.000
> >
> > BOND
> > o -c 570.0 1.229
> > c -h5 331.0 1.100
> > c -n 490.0 1.335
> > n -c3 337.0 1.449
> > c3-h1 330.0 1.060
> >
> > ANGLE
> > o -c -h5 0.000 121.59
> > o -c -n 00.00 121.90
> > c -n -c3 00.00 121.21
> > h5-c -n 0.000 116.60
> > n -c3-h1 0.000 109.47
> > c3-n -c3 0.000 116.8
> > h1-c3-h1 0.000 109.47
> >
> > DIHE
> > o -c -n -c3 1 2.500 180.00 2.000
> > c -n -c3-h1 1 0.000 0.00 2.000
> > h5-c -n -c3 1 2.500 180.00 2.000
> > c3-n -c3-h1 1 0.000 0.00 2.000
> >
> > IMPROPER
> > h5-n -c -o 1.1 180.0 2.0
> > c -c3-n -c3 1.1 180.0 2.0
> >
> > NONBON
> > o 1.72 0.210
> > c 1.93 0.105
> > h5 1.55 0.015
> > n 1.80 0.170
> > c3 1.87 0.066
> >
> >
> > min.in
> > minimization
> > &cntrl
> > imin=1, maxcyc=1000, ncyc=500, cut=900,
> > ntb=0, ntc=1, ntf=1, ntpr=10,ntwx=10,
> > ntp=0, tempi=293, temp0=293,
> > /
>
>
>
>
>
> ------------------------------
>
> Message: 16
> Date: Wed, 30 Oct 2013 08:52:10 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Free binding energy calculations for Zinc
> dependent ligands
> To: Tivani Mashamba <tivanim.yahoo.co.uk>, AMBER Mailing List
> <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3pDAadhSpZf0gjquoxQdZ+vQJRDe0BsBzLBesJcA4NvQA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Oct 30, 2013 at 5:09 AM, Tivani Mashamba <tivanim.yahoo.co.uk
> >wrote:
>
> >
> > Hi
> > I am trying to calculate binding free energy for Zinc dependent receptor:
> > ligand system, my receptor containd 2 Zinc atoms and the ligands are Zn
> > depedent. I have included the 2 Zn atoms in the SUB, see below:
> >
> > pirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i mmpbsa.in -o
> > mmpbsa.dat -sp com_solvated.top -cp com.top -rp rec.top -lp LIG.top -y
> > ZN1.top -lp ZN2.top -y md.mdcrd > mmpbsa.log
> >
> >
> > However, I am not getting any result and here is the error message that I
> > am getting.
> >
> > PrmtopError: Complex natom != receptor natom + ligand natom
> > Exiting. All files have been retained.
> >
>
> Your topology files are incompatible. One of the properties that MMPBSA.py
> checks is that there are as many atoms in the bound state (complex natom)
> as there are in the unbound state (receptor natom + ligand natom). Your
> topology files fail this test. You need to find out why your atom numbers
> do not match between your complex and receptor/ligand topology files and
> fix it.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 17
> Date: Wed, 30 Oct 2013 08:56:27 -0400
> From: Jose Borreguero <borreguero.gmail.com>
> Subject: Re: [AMBER] calculatie the energy between two groups of atoms
> from an MD trajectory, is it possible?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEee4gVizLNuDojDQi2Dr+LAczvtcUx=
> kXudwLQyiRxRooFHjQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thank you!
>
>
> On Tue, Oct 29, 2013 at 5:24 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > Three methods come to mind:
> >
> > 1) use cpptraj to strip out all but the atoms you want
> >
> > 2) use parmed to make a new prmtop with the only the interactions you
> want
> >
> > 3) if the energy is only a function of a few distances, extract those and
> > recompute it by hand
> >
> > All of those energies will likely be slightly different if you are using
> > PME, since then the energy isn't strictly pairwise in the reciprocal sum.
> >
> > Regards,
> > Brian
> >
> >
> > On Tue, Oct 29, 2013 at 4:37 PM, Jose Borreguero <borreguero.gmail.com
> > >wrote:
> >
> > > Dear Amber users,
> > >
> > > I was wondering whether it is possible to read and MD trajectory and
> > > calculate the energy between two groups of atoms, for instance, between
> > two
> > > nearby amino acids. From the manual, it seems that imin=5 will read the
> > > trajectory and output the energy of the whole system. Can one select
> the
> > > atoms for which Amber should calculate the energy?
> > >
> > > -Jose
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > 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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 18
> Date: Wed, 30 Oct 2013 09:12:50 -0400
> From: Pawel <pawelrc.gmail.com>
> Subject: Re: [AMBER] about rms atomic fluctuation for protein crystal
> .thank you very much!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <527105D2.7060108.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Aimee,
>
> To get the scaling properly you need something like this:
>
> A=40.000 #set this to the experimental value of your
> supercell's a-vector
> for frame in range(frames):
> a=celllen[frame,0] #get the a-vector of the current frame
> scale=a/A #scale factor (pressure scaling is isotropic in Amber
> so your scale factor will be the same in all dimensions
> currMoveVector=MoveVector*scale # scale your MoveVector
> coords[frame,:,:]=coords[frame,:,:]-MoveVector
>
> Try that and see what happens although if you are monitoring your volume
> and it is not deviating by more than 0.3% or so from the experimental,
> this should really not affect your B-factors all that much.
>
> Besides that I'm really not sure what the reason could be. Possibly the
> algorithm for fitting the unit cells (the least squares problem for
> finding the correct origin that I mentioned in previous e-mail) could
> have made a difference. Possibly your system is sampling an alternate
> ensemble that is producing different B-factors.
>
> Pawel
>
>
>
> On 10/29/2013 04:03 AM, Yongxiu Li wrote:
> > hello,Pawel
> > Thank you very much! I am so sorry for that I read the
> > RevSym_netcdf.py again and I think I have done the rescaling. I think
> > these lines do the all rescaling "
> > for frame in range(frames):
> > #get frame box
> > box=celllen[frame,:]
> > #convert to unit cell box
> > box=box/[ix,iy,iz]
> > #add angle information as provided by user
> > UCbox=hstack((box,SCBox[3:]))
> > #calc orthogonalization matrix
> > u,invu=CompXfrm(UCbox)
> > #matrix product
> > MoveVector=dot(invu,FracVector).astype(float32)
> > coords[frame,:,:]=coords[frame,:,:]-MoveVector
> > # reverse symmetry operate to original asym unit by
> > # applying the symmetry translation and rotation
> > coords[:,:,:]=dot( (coords[:,:,:]-t),linalg.inv(s) ) "
> > I'm not proficient in Python, so whether I understand is right? If
> > not, can you tell me how to do in python script? If I am right, I
> > still can't understand that compared with figure8 in Case's paper,why
> > the bfac_lat_calpha-arf.dat which I gained is so big.
> > btw,in the attachment is the lattice atomic root mean squared
> > fluctuations of a-carbons by amber ff99SB-tip3p.
> > Thank you very much!
> > Aimee Li
> >
> > Atomicrootmeansquared(rms)fluctuationsofa-carbons.
> >
> > On 10/16/2013 07:26 AM, Pawel wrote:
> >> Hi Aimee,
> >> On 10/15/2013 09:09 AM, Yongxiu Li wrote:
> >>> 1. if the "bfac_lat_calpha" in figure8 are calculated using a
> >>> different
> >>> approach than the one used in BasicAnalysis, how can I do it?
> >> If I understand correctly (I did not work on that paper myself), the
> >> alignment of asymmetric units was done by solving a least squares
> >> minimization problem to find (for each frame) the best location of the
> >> crystallographic origin in space so that after performing the
> >> appropriate symmetry operations and translations in reverse on each of
> >> the asymmetric units, the resulting RMSD between the asymmetric units
> >> would be minimized. Unfortunately I don't have the code for that
> >> approach. If it would be very useful to you, let me know and I'll
> >> investigate.
> >>
> >>> So as you said, I need to rescal coordinates.
> >>> However, after reading this paper I am confused that wether only
> >>> computing the lattice property (for example:rmsd_latt and
> >>> bfactor_latt)need rescal coordinates but computing the other
> >>> property(like rmsd_ASU ,bfactor_ASU and Distance deviation matrices)
> >>> needn't rescale the coordinates?
> >> If you are simulating an NPT ensemble, you should rescale the
> >> coordinates for all of these analyses. This should be done in
> >> RevSym_netcdf.py though I think the version of that script that you have
> >> does not do so. Like I said these scripts Analysis directory are all
> >> beta versions. However you should be able to do the rescaling easily by
> >> adding one or two line around line 95 of the script. If you have
> >> problems, let me know and I'll dig up a version that does this.
> >>
> >> Pawel
> >>
> >> _______________________________________________
> >> 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
>
>
>
> ------------------------------
>
> Message: 19
> Date: Wed, 30 Oct 2013 18:45:32 +0530
> From: Tanmoy Paul <tanmoy635.gmail.com>
> Subject: Re: [AMBER] optimization using gaussian and RESP using
> antechamber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAHTS+XhTapwfvHZk7RFm5HPYOJGvkjiq3mLAqFtpnH+8xtcOFA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> I would ask you to set iop(6/50=1) and then add two extra lines at the
> end of g09 input file.These two lines contains the name of the .esp file
> corresponding to the initial and optimised structure. Each line should be
> separated by one blank line.Then re-run the optimisation to generate the
> esp file. And then follow the instructions given in following link
> .............
>
>
>
> http://sf.anu.edu.au/collaborations/amber_on_fujitsu/amber-12/tutorial/nonstandard-setup/index.html
>
> Hope this will help
>
> Regards
>
> Tanmoy
>
>
> On Mon, Oct 21, 2013 at 4:59 PM, Bajarang Kumbhar <
> kumbharbajarang.gmail.com
> > wrote:
>
> > Hi
> >
> > recently i worked out for the geoemtry opitimization using G09 using
> SO4-2
> > group
> > but it woun't produce the prepin and frcmod file using antechamber.
> > %chk=SO4.chk
> > #P HF/6-31g* Opt
> > SOO4.pdb
> >
> > -2 1
> > S -0.00011283 0.00009246 -0.00011064
> > O 0.19932041 1.39283260 0.48010898
> > O -1.31262771 -0.10314457 -0.69076867
> > O 1.08864613 -0.35807868 -0.94726862
> > O 0.02488683 -0.93179428 1.15814958
> > --Link1--
> > %chk=SO4-1.chk
> > #P Opt HF/6-31G* SCF=Tight Geom=ALLCheck Guess=Read Pop=MK IOp(6/33=2,
> > 6/41=10, 6/42=17)
> >
> > using command
> > *antechamber -i SO4.log -fi gout -o SO4.prepi -fo prepin
> > -c resp*
> >
> > Info: Bond types are assigned for valence state 1 with penalty of 1
> >
> > Info: the number of the ESP exceeds the MAXESP(20000),extend the size and
> > reallocate the memory automatically
> > Info: the number of the ESP exceeds the MAXESP(30000),extend the size and
> > reallocate the memory automatically
> > *it runs but doesn't produced the correct prepin file using antechamber*
> >
> > i want to optimize using G09 and calculate the RESP.
> >
> >
> > Regards
> >
> >
> >
> > ---
> > Dr. Kumbhar Bajarang Vasant
> > M.Sc. Ph.D.
> > Bioinformatics Group,
> > Department of Biochemistry,
> > Shivaji University Kolhapur- 416004
> > (M.S.), India.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 20
> Date: Wed, 30 Oct 2013 16:34:26 -0200
> From: Fabr?cio Bracht <fabracht1.gmail.com>
> Subject: [AMBER] Hbond analysis
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAMRmCxs+heit1bcW5C7B8UsGPSiZGBqyo3hfHMiX1YGx4Pq10A.mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Hi, I have some doubts related to the hbond analysis results performed
> with cpptraj. I have specified the analysis along with the options for
> solvent hbond analysis and bridge. Within the hbond between residues, the
> interaction between a carboxylate from an asp residue and the hydrogens
> from the guanidinium group show up like this:
> ASP_204.OD2 ARG_206.HE ARG_206.NE 4228 0.8456
> 3.0151 145.4176
> ASP_204.OD1 ARG_206.HE ARG_206.NE 4072 0.8144
> 3.2199 154.9778
> So, the fraction of frames in which OD2 and OD1 stay bonded to the same
> hydrogen atom on arginine is 0.8456 and 0.8144 respectively. How can this
> be so? Shouldn?t the fractions add up to 1?
> I get even more confused when I take into account the other interactions
> that this asp residue does.
> ASP_204.OD2 OH1_342.H1 OH1_342.O 4612 0.9224
> 2.9481 158.4453
> This is OD2 bonded to a water molecule bound to a zinc complex.
> In the solvent analysis output.
> OH1_342.O SolventH SolventDnr 10182 2.0364
> 2.7305 162.2674
> How can the Hbond appear in 10182 frames if I only analysed 5000?
> Thank you in advance
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 659, Issue 1
> *************************************
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 30 2013 - 23:30:02 PDT
