[AMBER] prmtop file

From: Chandrasekaran, Suryanarayanan <s.chandrasekaran.jacobs-university.de>
Date: Tue, 11 Dec 2012 10:01:51 +0000

________________________________________
From: Chandrasekaran, Suryanarayanan
Sent: Tuesday, December 11, 2012 1:35 AM
To: amber.ambermd.org
Subject: prmtop file

  12. prmtop file (Chandrasekaran, Suryanarayanan)
  13. Re: prmtop file (Bill Miller III)

Hi Bill Miller,

Thank you for your reply, I dont find a specific command option for selecting a residue, i need to strip out water and do one by one, is there any specific command in Parmed.py to select the residue directly to write its property,
I dont need the file only for visualization, i need to run MD using that .prmtop. if u have any tutorial on extracting residue will be more helpful.

thnk u
surya
------------------------------

Message: 12
Date: Mon, 10 Dec 2012 12:04:46 +0000
From: "Chandrasekaran, Suryanarayanan"
        <s.chandrasekaran.jacobs-university.de>
Subject: [AMBER] prmtop file
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
        <3CEC60BEA7B5594D861FEB44BCE7CB4D2D8061.SXCHMB01.jacobs.jacobs-university.de>

Content-Type: text/plain; charset="iso-8859-1"


________________________________
From: Chandrasekaran, Suryanarayanan [s.chandrasekaran.jacobs-university.de]
Sent: Monday, December 10, 2012 1:01 PM
To: amber.ambermd.org
Subject:

HI

I need to create .prmtop file for a metal complex residue for bacteriochlorophyll(BCL) complex present in FMO protein, but i got the .prmtop file from another group and they asked us to use protein pdb file insted of .inpcrd file and its working fine for us in "namd", but i need to create .prmtop for the sigle residue BCL. is it possible to extract .prmtop files for a residue from a complete protein .prmtop file. but i dont have .inpcrd insted i have only .pdb file for whole system and for that residue.

otherwise is it possible to create .lib file for that residue from full protein .prmtop file.

thank you
surya


------------------------------

Message: 13
Date: Mon, 10 Dec 2012 07:26:46 -0500
From: Bill Miller III <brmilleriii.gmail.com>
Subject: Re: [AMBER] prmtop file
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <080A82D2-E141-4594-9001-0B3E7AEE81F4.gmail.com>
Content-Type: text/plain; charset=us-ascii

You can create a single residue prmtop from the complex using Parmed.py released with AmberTools.

-Bill

On Dec 10, 2012, at 7:04 AM, "Chandrasekaran, Suryanarayanan" <s.chandrasekaran.jacobs-university.de> wrote:

>
> ________________________________
> From: Chandrasekaran, Suryanarayanan [s.chandrasekaran.jacobs-university.de]
> Sent: Monday, December 10, 2012 1:01 PM
> To: amber.ambermd.org
> Subject:
>
> HI
>
> I need to create .prmtop file for a metal complex residue for bacteriochlorophyll(BCL) complex present in FMO protein, but i got the .prmtop file from another group and they asked us to use protein pdb file insted of .inpcrd file and its working fine for us in "namd", but i need to create .prmtop for the sigle residue BCL. is it possible to extract .prmtop files for a residue from a complete protein .prmtop file. but i dont have .inpcrd insted i have only .pdb file for whole system and for that residue.
>
> otherwise is it possible to create .lib file for that residue from full protein .prmtop file.
>
> thank you
> surya
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



------------------------------

Message: 14
Date: Mon, 10 Dec 2012 08:39:55 -0500
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Getting error messages during testing the
        installation.
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20121210133955.GB37946.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Mon, Dec 10, 2012, Sanjib Paul wrote:

> $CUDA_HOME is properly set. It is
> $CUDA_HOME=/usr/local/cuda. And libcurand.so.4 is in the directories I
> specify by the LD_LIBRARY_PATH. libcurand.so.4 is in the
> /usr/local/cuda/lib64 and in /usr/local/cuda/lib. And I set the
> LD_LIBRARY_PATH as export
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64. I did
> these things before my first mail and got those errors. Now what should I
> do?

Others on the list may know flags that give more detailed error messages.
I'd certainly recompile a fresh version, and make sure that the exectable
image you are running is the one you intend to run. You could try making a
static executable, but that is probably going in the wrong direction. I don't
know what would be causing the error below if the shared library is indeed in
the LD_LIBRARY_PATH.

> > > >> 1) "......: error while loading shared libraries: libcurand.so.4:
> > cannot
> > > >> open shared object file: No such file or directory".

...dac




------------------------------

Message: 15
Date: Mon, 10 Dec 2012 08:49:44 -0500
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Any possibility of scripting in tleap?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20121210134944.GC37946.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Mon, Dec 10, 2012, Sajeewa Pemasinghe wrote:
>
> I have to run the same 3 commands on about 200 pdb files which are like
> cdd1.pdb ,cdd2.pdb, cdd3.pdb.......cdd200.pdb. Is there any way I can get
> this run by a script like (rough)
>
> for(int i=0;i<200;i++){
>
> command1 cddi.pdb
> command2 cddi.pdb
> command3 cddi.pdb
>
> }

Shells can do this; see, e.g.
http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html for info on how to make a
loop in the bash shell. It would look something like this (untested!)

  for i in `seq 1 200`; do
     command1 cdd$i.pdb
     command2 cdd$i.pdb
     command3 cdd$i.pdb
  done

Learning shell scripts is well worth your time. (Note that your text
indicated that you wanted to have i go from 1 to 200, but your sample code
looped from 0 to 199; be sure to write you really want.)

...dac




------------------------------

Message: 16
Date: Mon, 10 Dec 2012 08:56:02 -0500
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Problem with molecule containing sulfonic acid
        substitution
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20121210135602.GD37946.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Mon, Dec 10, 2012, Bernhard Poll wrote:
>
> I got some problems simulating a molecule containing a sulfonic acid
> substitution. The simulation aborts during the pre-processing heat-up
> giving no error in the heat.out (it writes the first line of the heat-up
> process (NSTEP= 0 TIME (PS) = 0.000 etc.) in section 4.results in the
> heat.out).

Usual debugging advice: run a short test with ntpr=1 and nstlim=20. Try it
with both cpu and gpu codes. In this way you can try to narrow down the
source of the problem. If you find things like very bad energies or
temperatures, examine the molecule gometry, looking especially at positions
of the hydrogens in your sulfonic acid -- maybe they are getting too close
to oxygen atoms.

...dac




------------------------------

Message: 17
Date: Mon, 10 Dec 2012 15:14:33 +0100
From: davide branduardi <davide.branduardi.gmail.com>
Subject: Re: [AMBER] Amber12 with Plumed
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAEHxBqnWAcOtFjev_uWOE6LH0hEoX0kwTzyYS0Bwv2dA_Dwq4A.mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

Dear Rajeswari,
  I am one of plumed developers and there are no project active from us
that involve amber12 (AFAIK). For that reason we just support only amber11.
Nevertheless you can try out to hack sander at your own peril. I did not
find any major problem in moving from
version 10 to 11 but I do not know about 12. Might be that it is as simple.
A good starting point is the following:
- take a old version of amber that is supported by plumed and make a test (
a simple umbrella sampling or metadynamics) on a simple system and store
the result.
-patch the new sander code with plumed: check if all the procedure goes
well (i.e. do you get any FAIL for the patching? does the script find the
patch tool?). If you overlook this stage it might well be that the program
compiles but WITHOUT plumed!! This might be your case since it looks like
the command line is not recognized.
If it fails try to check the code (.rej files), compare the patched
previous version with actual sander and try to figure out an equivalent
position for the plumed calls in the source (they are not many, probably 3
or 4, it should not be a big deal) and try to patch the code "by hand"
-make the test and see if you get any PLUMED.OUT file in output and if your
outputs coincide with the previous version.
Hope it helps!
Good luck!
Davide

PS: a useful thing is to post these question in plumed-user mailing list as
well!




On Mon, Dec 10, 2012 at 11:32 AM, Rajeswari A.
<rajeswari.biotech.gmail.com>wrote:

> Dear amberusers,
> I want to know whether Plumed 1.3 is compatible with amber12? i installed
> amber 12 along with plumed1.3. During installation there was no error
> message. But all plumed tests were failed and for my own system when i run
> sander with plumed, it says "error in reading namelist cntrl". my input
> file is below which has additional 2flags for plumed.
>
> &cntrl
> imin = 0, ntx = 7, irest = 1,
> ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
> ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> nstlim = 500000, dt =0.002,
> tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> plumed=1 , plumedfile=?plumed.dat?
> &end
>
> Waiting for your response!
>
> Thank you,
> Rajeswari A
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


------------------------------

Message: 18
Date: Mon, 10 Dec 2012 09:35:57 -0500
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Subject: Re: [AMBER] Any possibility of scripting in tleap?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAMU91jpgH1zgPVG-4dcmNBu+id8ik+F6B7rTeY3xzBy+HwRqGA.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Thank you very much Dr.Case. Thank you for correcting me. Yes I should have
used (i+1) OR for(int i=1;i<201;i++){........

On Mon, Dec 10, 2012 at 8:49 AM, David A Case <case.biomaps.rutgers.edu>wrote:

> On Mon, Dec 10, 2012, Sajeewa Pemasinghe wrote:
> >
> > I have to run the same 3 commands on about 200 pdb files which are like
> > cdd1.pdb ,cdd2.pdb, cdd3.pdb.......cdd200.pdb. Is there any way I can get
> > this run by a script like (rough)
> >
> > for(int i=0;i<200;i++){
> >
> > command1 cddi.pdb
> > command2 cddi.pdb
> > command3 cddi.pdb
> >
> > }
>
> Shells can do this; see, e.g.
> http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html for info on how to
> make a
> loop in the bash shell. It would look something like this (untested!)
>
> for i in `seq 1 200`; do
> command1 cdd$i.pdb
> command2 cdd$i.pdb
> command3 cdd$i.pdb
> done
>
> Learning shell scripts is well worth your time. (Note that your text
> indicated that you wanted to have i go from 1 to 200, but your sample code
> looped from 0 to 199; be sure to write you really want.)
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


------------------------------

Message: 19
Date: Mon, 10 Dec 2012 20:10:40 +0530
From: "Rajeswari A." <rajeswari.biotech.gmail.com>
Subject: Re: [AMBER] Amber12 with Plumed
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAOzJmL_G624C9UVZiJuY4BvkjHxKpDHR6ARj+f1d3e6yn5uBNw.mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

Dear Davide,
I thank you very much for your quick and elaborate reply. Surely i will try
your suggestions and reply you.

Thanks a lot
Rajeswari

On Mon, Dec 10, 2012 at 7:44 PM, davide branduardi <
davide.branduardi.gmail.com> wrote:

> Dear Rajeswari,
> I am one of plumed developers and there are no project active from us
> that involve amber12 (AFAIK). For that reason we just support only amber11.
> Nevertheless you can try out to hack sander at your own peril. I did not
> find any major problem in moving from
> version 10 to 11 but I do not know about 12. Might be that it is as simple.
> A good starting point is the following:
> - take a old version of amber that is supported by plumed and make a test (
> a simple umbrella sampling or metadynamics) on a simple system and store
> the result.
> -patch the new sander code with plumed: check if all the procedure goes
> well (i.e. do you get any FAIL for the patching? does the script find the
> patch tool?). If you overlook this stage it might well be that the program
> compiles but WITHOUT plumed!! This might be your case since it looks like
> the command line is not recognized.
> If it fails try to check the code (.rej files), compare the patched
> previous version with actual sander and try to figure out an equivalent
> position for the plumed calls in the source (they are not many, probably 3
> or 4, it should not be a big deal) and try to patch the code "by hand"
> -make the test and see if you get any PLUMED.OUT file in output and if your
> outputs coincide with the previous version.
> Hope it helps!
> Good luck!
> Davide
>
> PS: a useful thing is to post these question in plumed-user mailing list as
> well!
>
>
>
>
> On Mon, Dec 10, 2012 at 11:32 AM, Rajeswari A.
> <rajeswari.biotech.gmail.com>wrote:
>
> > Dear amberusers,
> > I want to know whether Plumed 1.3 is compatible with amber12? i installed
> > amber 12 along with plumed1.3. During installation there was no error
> > message. But all plumed tests were failed and for my own system when i
> run
> > sander with plumed, it says "error in reading namelist cntrl". my input
> > file is below which has additional 2flags for plumed.
> >
> > &cntrl
> > imin = 0, ntx = 7, irest = 1,
> > ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
> > ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> > nstlim = 500000, dt =0.002,
> > tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> > ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> > plumed=1 , plumedfile=?plumed.dat?
> > &end
> >
> > Waiting for your response!
> >
> > Thank you,
> > Rajeswari A
> > _______________________________________________
> > 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: 20
Date: Mon, 10 Dec 2012 10:44:19 -0500
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] enthalpy and sum of per residue energy
        decomposition not euqal
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAEk9e3rxsFFqxJL=_9SqnG-hp6N326j-4BML4x+cMCm=3syFiw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Mon, Dec 10, 2012 at 4:09 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:

>
> Hello All
> I am doing MMPBSA analysis of protein-DNA complex.
> I want to ask a question that why sum of energy of all residue by per
> residue
> energy decomposition is not equal to enthalpy of complex though both have
> same
> energy component?
> In my case sum of energy of all residue is -119.6 kcal/mol and enthalpy of
> complex is 130.4 kcal/mol.
>
> When I checked for MMPBSA tutorial there also two value are not equal
>

No, they should not be equal. By adding up all per-residue contributions,
you are significantly double-counting the non-bonded interactions.
 Consider two atoms in different residues. Their interaction should be
counted toward the decomposed, per-residue energy of both residues, but it
should only be included once in the total energy.

Since residues have internal non-bonded interactions, extracting the exact
total energy from the decomposition results is non-trivial.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
------------------------------
Message: 21
Date: Tue, 11 Dec 2012 00:02:52 +0800 (CST)
From: "Mu Xia" <muxiachuixue.163.com>
Subject: [AMBER] Problem in Nmode entropy calculation
To: Amber <amber.ambermd.org>
Message-ID: <21463580.c45.13b858dfbaa.Coremail.muxiachuixue.163.com>
Content-Type: text/plain; charset=GBK
Hi everyone:
I am calculating normal mode entropy using amber11.
System info:
342 residues protein
1 ligand
Below is my input file:
___________________________________________
Input file for running entropy calculations using NMode
&general
   startframe=4001, endframe=5000, keep_files=2, interval=10,
/
&nmode
   nmstartframe=1,
   nminterval=10, nmode_igb=1, nmode_istrng=0.1,
/
# Execute the program
mpirun -np 8 MMPBSA.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp A-WFE-sol.prmtop -cp A-WFE-nw.prmtop -rp A-nc.prmtop -lp wfe.prmtop -y A-WFE-sol-md9.mdcrd > progress.log 2>&1 &
_________________________________________________
Output file:
_________________________________________________
Running MMPBSA.MPI on 8 processors...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/Amber/amber11/bin/ptraj
nmode program found! Using /home/Amber/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
100 frames were read in and processed by ptraj for use in calculation.
Beginning nmode calculations with mmpbsa_py_nabnmode...
Master thread is calculating normal modes for 2 frames
  calculating complex  contribution for frame 0
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
____________________________________________
_MMPBSA_complex_nm.out output file :
===============================================
Reading parm file (A-WFE-nw.prmtop)
title:
mm_options:  ntpr=10000
mm_options:  diel=C
mm_options:  kappa=0.103951911959
mm_options:  cut=1000
mm_options:  gb=1
mm_options:  dielc=4.0
mm_options:  temp0=298.15
mm_options:  wcons=0
scaling charges by    0.500
      iter    Total       bad      vdW     elect   nonpolar   genBorn      frms
ff:     0 6230417012595346944821921232222945280.00 1678292.63 6230417012595346944821921232222945280.00 -69535.11      0.00   -111.95  3.65e+38
________________________________________________________________
 MIN:          It=    0  nfunc=     1  E= 6230417012595346944821921232222945280.00000 ( 3.65e+38)
  CG:   It=    3 (  0.001)q  :-)
  LS: i= 1  lhs_f=  -3.6909588e+36  rhs_f=  -5.8070789e+32
            lhs_g=   2.1955886e+36  rhs_g=    5.226371e+36
  LS: step=               1  it= 1
 MIN:          It=    1  nfunc=     5  E= 2539441597772510129576161609305292800.00000 ( 1.38e+38)
  CG:   It=    1 (999.999)q  :-((
  LS: i= 1  lhs_f=  -1.4970485e+36  rhs_f=  -2.3477617e+32
            lhs_g=   8.9439214e+35  rhs_g=   2.1129855e+36
  LS: step=               1  it= 1
 MIN:          It=    2  nfunc=     8  E= 1042327953959392618393314531324461056.00000 ( 5.25e+37)
  CG:   It=    0 (999.999)q  :-((
  LS: i= 1  lhs_f=  -1.0383955e+36  rhs_f=  -1.6128561e+35
            lhs_g=   7.6150276e+72  rhs_g=   4.1582959e+79
  LS: step=    3.490782e-41  it= 1
 MIN:          It=    3  nfunc=    10  E= 2442916330927895292876510610849792.00000 ( 1.95e+34)
  CG:   It=    3 (  0.083)q  :-)
  LS: i= 1  lhs_f=  -1.3877588e+33  rhs_f=  -2.1772565e+29
            lhs_g=   8.3000993e+32  rhs_g=   1.9595308e+33
  LS: step=               1  it= 1
Please anybody could help me understand what is going on and help giving solution to this issue?
Thanks
Shifeng Chen
------------------------------
Message: 22
Date: Mon, 10 Dec 2012 11:29:57 -0500
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Force calculation during SMD (jar=1): I'm looking
        for     insights
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAEk9e3r2Jt=5kSABgwniYizxFFixYAKYtpXPS=f47dazdqDVbQ.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, Dec 10, 2012 at 5:31 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Hello,
>
> I am wondering how forces with jar=1 are actually calculated in case of
> a distance restraint between two atoms. The way I understand it, a
> 'correctional' force is dynamically calculated with each MD time step
> and applied in order to force the distance d between two atoms on a
> certain trajectory d(t), which is a linear relation in this case.
>
> In sander's nmr.F90, I've found `fcurr = -2.0*rk2*(rint-r2)` (line 3778
> for Amber 12).
>
The forces with jar==1 are calculated the same way as the forces with
nmropt==1 (e.g., as with umbrella sampling)--as in, they use the same
subroutine calls.  The difference with jar=1 is that you also have to
accumulate the work done by the moving potential.  Since work is not a
vector (it's the inner product of the force and position vectors), it has
no direction.
> First of all, I am wondering about the direction of the force. I'm not a
> Fortran expert, but assuming all of the variables in the code line above
> are scalars, only the force magnitude is calculated here. The direction
> should be given by the gradient of the according potential. Where/how is
> the direction of the force calculated?
>
The variables you quoted above are part of the work calculation, not the
force calculation.  Hence, no direction ;).  The forces and energies are
calculated in different subroutines on a per-restraint basis.  If you are
looking for a distance, look for the subroutine "disnrg" in nmr.F90.  This
is where the force (and its direction) are calculated.  The direction comes
at the end, where dfr(m) is calculated.  Note that xij is a vector (since
it is just xi-xj), which gives the direction and magnitude in each (x, y,
and z) direction.  Also note that, as per Newton's 3rd law, that the force
exerted by the restraint on the first atom is the same, but opposite of
that on the second atom.  In this subroutine, f() is the force array.
The code is a bit convoluted due to the numerous options and fairly complex
mathematical form of the restraint potential, but the ideas are still
there.  You can look at angnrg, tornrg, etc. for how the forces are
calculated and accumulated for the different types of restraints.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
------------------------------
Message: 23
Date: Mon, 10 Dec 2012 11:33:41 -0500
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Problem in Nmode entropy calculation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAEk9e3rn43Zo9i8gxquD76nU_7dvnLxAxe9Ee9nse=1FCmhsrw.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
It looks like you have a problem between your coordinate and topology
files.  Common things to look out for -- did you keep any waters in your
complex topology.  Ions?  Do you have any 'strange' ions?
Try visualizing your intermediate trajectories (_MMPBSA_complex.mdcrd,
_MMPBSA_receptor.mdcrd, and _MMPBSA_ligand.mdcrd) with the corresponding
topology files in VMD (or some other visualization program) to see if the
structures look horribly wrong.
Also look at the default strip_mask definition (in the Amber manual).  You
may have to modify this if you have 'weird' ions in your system.
Good luck,
Jason
On Mon, Dec 10, 2012 at 11:02 AM, Mu Xia <muxiachuixue.163.com> wrote:
> Hi everyone:
>
>
> I am calculating normal mode entropy using amber11.
>
>
> System info:
> 342 residues protein
> 1 ligand
>
>
> Below is my input file:
> ___________________________________________
> Input file for running entropy calculations using NMode
> &general
>    startframe=4001, endframe=5000, keep_files=2, interval=10,
> /
> &nmode
>    nmstartframe=1,
>    nminterval=10, nmode_igb=1, nmode_istrng=0.1,
> /
>
>
> # Execute the program
> mpirun -np 8 MMPBSA.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> A-WFE-sol.prmtop -cp A-WFE-nw.prmtop -rp A-nc.prmtop -lp wfe.prmtop -y
> A-WFE-sol-md9.mdcrd > progress.log 2>&1 &
> _________________________________________________
>
>
> Output file:
>
>
> _________________________________________________
> Running MMPBSA.MPI on 8 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/Amber/amber11/bin/ptraj
> nmode program found! Using /home/Amber/amber11/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation...
> 100 frames were read in and processed by ptraj for use in calculation.
>
>
> Beginning nmode calculations with mmpbsa_py_nabnmode...
> Master thread is calculating normal modes for 2 frames
>
>
>   calculating complex  contribution for frame 0
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> Line minimizer aborted: step at lower bound
> ____________________________________________
>
>
> _MMPBSA_complex_nm.out output file :
>
>
> ===============================================
> Reading parm file (A-WFE-nw.prmtop)
> title:
>
> mm_options:  ntpr=10000
> mm_options:  diel=C
> mm_options:  kappa=0.103951911959
> mm_options:  cut=1000
> mm_options:  gb=1
> mm_options:  dielc=4.0
> mm_options:  temp0=298.15
> mm_options:  wcons=0
> scaling charges by    0.500
>       iter    Total       bad      vdW     elect   nonpolar   genBorn
>  frms
> ff:     0 6230417012595346944821921232222945280.00 1678292.63
> 6230417012595346944821921232222945280.00 -69535.11      0.00   -111.95
>  3.65e+38
> ________________________________________________________________
>  MIN:          It=    0  nfunc=     1  E=
> 6230417012595346944821921232222945280.00000 ( 3.65e+38)
>   CG:   It=    3 (  0.001)q  :-)
>   LS: i= 1  lhs_f=  -3.6909588e+36  rhs_f=  -5.8070789e+32
>             lhs_g=   2.1955886e+36  rhs_g=    5.226371e+36
>   LS: step=               1  it= 1
>  MIN:          It=    1  nfunc=     5  E=
> 2539441597772510129576161609305292800.00000 ( 1.38e+38)
>   CG:   It=    1 (999.999)q  :-((
>   LS: i= 1  lhs_f=  -1.4970485e+36  rhs_f=  -2.3477617e+32
>             lhs_g=   8.9439214e+35  rhs_g=   2.1129855e+36
>   LS: step=               1  it= 1
>  MIN:          It=    2  nfunc=     8  E=
> 1042327953959392618393314531324461056.00000 ( 5.25e+37)
>   CG:   It=    0 (999.999)q  :-((
>   LS: i= 1  lhs_f=  -1.0383955e+36  rhs_f=  -1.6128561e+35
>             lhs_g=   7.6150276e+72  rhs_g=   4.1582959e+79
>   LS: step=    3.490782e-41  it= 1
>  MIN:          It=    3  nfunc=    10  E=
> 2442916330927895292876510610849792.00000 ( 1.95e+34)
>   CG:   It=    3 (  0.083)q  :-)
>   LS: i= 1  lhs_f=  -1.3877588e+33  rhs_f=  -2.1772565e+29
>             lhs_g=   8.3000993e+32  rhs_g=   1.9595308e+33
>   LS: step=               1  it= 1
>
>
>
>
> Please anybody could help me understand what is going on and help giving
> solution to this issue?
>
>
> Thanks
>
>
> Shifeng Chen
> _______________________________________________
> 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
------------------------------
Message: 24
Date: Mon, 10 Dec 2012 16:43:17 +0000
From: ABEL Stephane 175950 <Stephane.ABEL.cea.fr>
Subject: [AMBER] GAFF atom types for the headgroup of the LDAO
        surfactant
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <3E39B768BB199548AB18F7289E7534AF02D3BD34.EXDAG0-B0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"
Hi all,
I would like to simulate LDAO surfactant with the GAFF parameters. However i have a doubt about the atom types N and O atoms of the amine-N-Oxide group,  I would like to use the GAFF atom types (N4 and O). I am not sure if it is  a good choice.
According to GAFF2b7 (gaff.dat in AMBER12)
n4 14.01         0.530               Sp3 N with four connected atoms
o  16.00         0.434               Oxygen with one connected atom
Could you help me ?
Stephane
------------------------------
Message: 25
Date: Mon, 10 Dec 2012 12:43:19 -0500
From: Ryan Pavlovicz <pavlovicz.7.osu.edu>
Subject: [AMBER] NAB nmode memory requirements
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAC9O94SS-cs8wOdFGt6HfFndrewv1v6+9HYAva6FRJ7F8ReUbg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I am trying to do some nmode calculations with nab (mpinab) on a system of
11,795 atoms.
>From what i understand, the nmode calculations would calculate a Hessian of
3Nx3N elements, and each element would take 8 bytes.
Therefore, my system of 11,795 atoms, 35,385 coordinates, and 1.25 million
matrix elements would need ~10 GB of memory. However, my testing on
supercomputer nodes with 48 GB of physical memory have been confusing. Some
of these jobs fail once they pass to the Newton Raphson part of the
calculation and memory requirements exceed 48 GB. However some of my jobs
are successful in completing a couple iterations of NR minimization before
walltime runs out. When monitoring these successful jobs, i see that they
are using ~211 GB of memory to complete these calculations.
Is my estimation of required memory off by ~200 GB or is there a potential
problem with the mpinab executable i am using?
Thanks for your help,
ryan
input file, nmode_complex.nab:
molecule m;
float x[35385], fret;
m = getpdb("../../../com1.pdb");
readparm(m, "../../../complex.prmtop");
getxyz("../../../snaps/BigD_2_1_com.crd.1",11795,x);
mm_options("cut=999.0, ntpr=1, nsnb=99999, diel=C, gb=1, dielc=1.0");
mme_init(m, NULL, "::Z", x, NULL);
setxyz_from_mol(m, NULL, x);
//conjugate gradient minimization
conjgrad(x,3*m.natoms,fret,mme,0.001,0.001,20000);
//newton-raphson minimization
newton(x,3*m.natoms,fret,mme,mme2,0.0000001,0.0,1000);
//get normal modes
nmode(x,3*m.natoms,mme2,0,0,0.0,0.0,0);
batch execution:
$AMBERHOME/bin/mpinab -o nmode_complex nmode_complex.nab
mpiexec ./nmode_complex > nmode_com1.out
------------------------------
Message: 26
Date: Mon, 10 Dec 2012 12:51:48 -0500
From: Yulin Huang <yulinhuang2007.gmail.com>
Subject: Re: [AMBER] For TI do corresponding same atoms in ligand
        pairs need to have the same charge
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CA+JH+ZYXr19NPefK8GpuyphpexqxpyuzpEHcJR1mh-+9Zq_GGg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
  Dear Amber community,
           Thanks for all your previous help.  I want to restate my problem
more clearly.
 For states V0 and V1 unperturbed atoms (in other words, the same atoms
with the same coordinates), do they need to have exactly the same charges?
It seems that for V0 ->V1, V1 may copy the charges from V0 and for V1->V0,
V0 may copy the charges from V1.  This may lead to the wrong Hamiltonian.
          I guess I need to make the unperturbed atoms have exactly the
same charges.  The way to do this is to change the charges of the perturbed
atoms to make the formal charges the same.
         Could anyone give me some comments over this issue?  Many thanks
in advance.
Yulin
On Sat, Dec 8, 2012 at 10:13 PM, Yulin Huang <yulinhuang2007.gmail.com>wrote:
> Hi, Professor David Case. Thank you so much for your reply.
>
> Yulin
>
>
> On Sat, Dec 8, 2012 at 10:03 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Sat, Dec 08, 2012, Yulin Huang wrote:
>>
>> >          For thermodynamic integration, do corresponding same atoms in
>> > ligand pairs need to have the same charge?
>>
>> No.  For most changes of interest, corresponding atoms in V0 and V1 would
>> in
>> fact *not* have the same charge.
>>
>> > It seems that it may affect the energy calculation.
>>
>> Indeed.
>>
>> ...good luck...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Yulin "Joyce" Huang
> Ph.D Candidate
> Computational Chemistry (CADD)
> Advisor: Dr. Robert C. Rizzo
> State University of New York at Stony Brook
> Stony Brook NY,11790
> Office: (631)632-8519
>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
------------------------------
Message: 27
Date: Tue, 11 Dec 2012 00:04:08 +0530 (IST)
From: "Sangita Kachhap" <sangita.imtech.res.in>
Subject: Re: [AMBER] enthalpy and sum of per residue energy
        decomposition not euqal
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID: <54637.125.19.68.203.1355164448.squirrel.172.141.121.65>
Content-Type: text/plain;charset=utf-8
Thank you Jason for explanation.
> On Mon, Dec 10, 2012 at 4:09 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello All
>> I am doing MMPBSA analysis of protein-DNA complex.
>> I want to ask a question that why sum of energy of all residue by per
>> residue
>> energy decomposition is not equal to enthalpy of complex though both have
>> same
>> energy component?
>> In my case sum of energy of all residue is -119.6 kcal/mol and enthalpy of
>> complex is 130.4 kcal/mol.
>>
>> When I checked for MMPBSA tutorial there also two value are not equal
>>
>
> No, they should not be equal.  By adding up all per-residue contributions,
> you are significantly double-counting the non-bonded interactions.
>  Consider two atoms in different residues.  Their interaction should be
> counted toward the decomposed, per-residue energy of both residues, but it
> should only be included once in the total energy.
>
> Since residues have internal non-bonded interactions, extracting the exact
> total energy from the decomposition results is non-trivial.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
?????????? ???????????? ??????? (????????? ???????? ???????? ?????)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
?????? 39 ?, ???????? / Sector 39-A, Chandigarh
??? ???/PIN CODE :160036
??????/EPABX :0172 6665 201-202
------------------------------
Message: 28
Date: Mon, 10 Dec 2012 14:14:15 -0500
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] NAB nmode memory requirements
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20121210191415.GB39744.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Mon, Dec 10, 2012, Ryan Pavlovicz wrote:
> I am trying to do some nmode calculations with nab (mpinab) on a system of
> 11,795 atoms.
>
> >From what i understand, the nmode calculations would calculate a Hessian of
> 3Nx3N elements, and each element would take 8 bytes.
>
> Therefore, my system of 11,795 atoms, 35,385 coordinates, and 1.25 million
> matrix elements would need ~10 GB of memory. However, my testing on
> supercomputer nodes with 48 GB of physical memory have been confusing. Some
> of these jobs fail once they pass to the Newton Raphson part of the
> calculation and memory requirements exceed 48 GB. However some of my jobs
> are successful in completing a couple iterations of NR minimization before
> walltime runs out. When monitoring these successful jobs, i see that they
> are using ~211 GB of memory to complete these calculations.
>
> Is my estimation of required memory off by ~200 GB or is there a potential
> problem with the mpinab executable i am using?
I'd suggest avoiding the NR step: you can generally minimize to an acceptably
low gradient just with xmin: just be patient (i.e. expect to use lots of steps
of minimization.)  This will be faster and will avoid potentially needing
space for both NR and normal modes in the same job.
If I remember correctly, you can use putxyz() and getxyz() to save coordinates
in high-precision, so you can minimize in one job, then read those coords back
in to continue with a vibrational calculation in a separate job.
...dac
p.s.: you have *lots* of atoms.  I personally have never done a normal mode
calculation this big.
------------------------------
Message: 29
Date: Mon, 10 Dec 2012 14:26:08 -0500 (EST)
From: steinbrt.rci.rutgers.edu
Subject: Re: [AMBER] For TI do corresponding same atoms in ligand
        pairs need to have the same charge
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID:
        <58b3b62295b93463692c24a19f9bd725.squirrel.webmail.rci.rutgers.edu>
Content-Type: text/plain;charset=iso-8859-1
Hi,
>  For states V0 and V1 unperturbed atoms (in other words, the same atoms
> with the same coordinates), do they need to have exactly the same charges?
no, they can but don't have to. This means implicitly that if they do not
have the same charge, your transformation free energy accounts for
changing this charge, plus whatever else is changing in the unique atoms.
The common atom electrostatics is scaled linearly, but that is normally
not a reason for concern.
So you need to make sure to compute free energy changes in which the
overall charge changes cancel out, since they do not contribute meaningful
total energy terms.
Doing the same transformation (e.g. between two ligands with differing
charges) in two environments (e.g. in two different solvents) yields
cancelling internal electrostatics terms and meaningful delta-delta-Gs
So typically, having different charges on common atoms is something that
will occur in your simulations, that will influence dVdl and that is fine
:-)
Thomas
------------------------------
Message: 30
Date: Mon, 10 Dec 2012 14:28:37 -0500
From: Yulin Huang <yulinhuang2007.gmail.com>
Subject: Re: [AMBER] For TI do corresponding same atoms in ligand
        pairs need to have the same charge
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CA+JH+ZYP34gLVY5hWJYkzAEs1JcUAC1W1+kH0oqkh6jJhAnoNg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi, Thomas.  Thank you so much for your detailed explanation.
Yulin
On Mon, Dec 10, 2012 at 2:26 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> >  For states V0 and V1 unperturbed atoms (in other words, the same atoms
> > with the same coordinates), do they need to have exactly the same
> charges?
>
> no, they can but don't have to. This means implicitly that if they do not
> have the same charge, your transformation free energy accounts for
> changing this charge, plus whatever else is changing in the unique atoms.
> The common atom electrostatics is scaled linearly, but that is normally
> not a reason for concern.
>
> So you need to make sure to compute free energy changes in which the
> overall charge changes cancel out, since they do not contribute meaningful
> total energy terms.
>
> Doing the same transformation (e.g. between two ligands with differing
> charges) in two environments (e.g. in two different solvents) yields
> cancelling internal electrostatics terms and meaningful delta-delta-Gs
>
> So typically, having different charges on common atoms is something that
> will occur in your simulations, that will influence dVdl and that is fine
> :-)
>
> Thomas
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
------------------------------
Message: 31
Date: Mon, 10 Dec 2012 14:45:30 -0500
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] For TI do corresponding same atoms in ligand
        pairs need      to have the same charge
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20121210194529.GC39744.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Mon, Dec 10, 2012, Yulin Huang wrote:
>  For states V0 and V1 unperturbed atoms (in other words, the same atoms
> with the same coordinates), do they need to have exactly the same charges?
> It seems that for V0 ->V1, V1 may copy the charges from V0 and for V1->V0,
> V0 may copy the charges from V1.  This may lead to the wrong Hamiltonian.
I think there is a nomenclature problem here:  TI has no conception of
what is a "perturbed" or an "unperturbed" atom.  It simply computes the
energy difference between the V0 and the V1 states of the entire system.
I'd think of an atom that is changing its charge as being "perturbed", but the
program doesn't keep any such list.
I'd be curious to know what it is that makes you think that "V1 may copy the
charges from V0".  As far as I can see, nothing like this takes place.
Note also that with softcore, there *is* a distinction between
"appearing/disappearing" atoms (which exist in one prmtop file but no the
other) and common atoms (which exist in both prmtop files).  Common atoms
don't need to have the same charges in the two endpoints.
[Aside: "appearing/disappearing" is actually a bad choice of wording; such
atoms are decoupled from their surroundings during the TI process--they don't
actually disappear.]
...dac
------------------------------
Message: 32
Date: Mon, 10 Dec 2012 14:51:13 -0500
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] NAB nmode memory requirements
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAEk9e3pH+SsAuc43iz7dnNj9qpqQruCem0fVRexc_MjPMZgVPg.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
In addition to what Dave said, I would suggest against using mpinab.  If
you desire parallelism that much, go with OpenMP instead.  The problem with
MPI in this case is that memory is not shared.  Each thread has its own
data, in addition to a buffer that is commonly used for MPI operations,
like reductions and gathers.  Therefore, for MPI I think you can expect
each thread to use 9.5 GB of RAM, including perhaps a second copy of the
Hessian for a MPI_Reduce.  All told, if I assume you have 16 cores on your
node with 48 GB, I would expect your job to need ~150 GB of RAM.
If someone tried parallelizing the construction of the hessian and added a
reduce buffer to collect the contributions from each node, go ahead and
double this to get ~300 GB.
Of course the flaw in the above analysis is that I think NAB takes
advantage of the fact that the Hessian is symmetric, so it only needs to
store the upper triangular portion of the matrix in addition to the
diagonal elements, cutting the memory requirements (almost) in half.  Of
course, the BLAS routines responsible for diagonalizing the Hessian needs
some scratch space allocated for the calculation, which would seem
reasonable to me that the memory requirements jump back to the 200 GB range.
OpenMP, on the other hand, uses shared memory parallelism, often
eliminating the need for separate copies of each array.  The best option
here, IMO, is to follow Dave's advice and separate the minimization/normal
mode steps, in which you can reasonably expect to use mpinab for the
minimization step before executing the normal mode calculation in serial.
HTH,
Jason
On Mon, Dec 10, 2012 at 12:43 PM, Ryan Pavlovicz <pavlovicz.7.osu.edu>wrote:
> I am trying to do some nmode calculations with nab (mpinab) on a system of
> 11,795 atoms.
>
> >From what i understand, the nmode calculations would calculate a Hessian
> of
> 3Nx3N elements, and each element would take 8 bytes.
>
> Therefore, my system of 11,795 atoms, 35,385 coordinates, and 1.25 million
> matrix elements would need ~10 GB of memory. However, my testing on
> supercomputer nodes with 48 GB of physical memory have been confusing. Some
> of these jobs fail once they pass to the Newton Raphson part of the
> calculation and memory requirements exceed 48 GB. However some of my jobs
> are successful in completing a couple iterations of NR minimization before
> walltime runs out. When monitoring these successful jobs, i see that they
> are using ~211 GB of memory to complete these calculations.
>
> Is my estimation of required memory off by ~200 GB or is there a potential
> problem with the mpinab executable i am using?
>
> Thanks for your help,
>
> ryan
>
> input file, nmode_complex.nab:
>
> molecule m;
> float x[35385], fret;
>
> m = getpdb("../../../com1.pdb");
> readparm(m, "../../../complex.prmtop");
> getxyz("../../../snaps/BigD_2_1_com.crd.1",11795,x);
>
> mm_options("cut=999.0, ntpr=1, nsnb=99999, diel=C, gb=1, dielc=1.0");
> mme_init(m, NULL, "::Z", x, NULL);
> setxyz_from_mol(m, NULL, x);
>
> //conjugate gradient minimization
> conjgrad(x,3*m.natoms,fret,mme,0.001,0.001,20000);
>
> //newton-raphson minimization
> newton(x,3*m.natoms,fret,mme,mme2,0.0000001,0.0,1000);
>
> //get normal modes
> nmode(x,3*m.natoms,mme2,0,0,0.0,0.0,0);
>
> batch execution:
>
> $AMBERHOME/bin/mpinab -o nmode_complex nmode_complex.nab
> mpiexec ./nmode_complex > nmode_com1.out
> _______________________________________________
> 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
------------------------------
Message: 33
Date: Mon, 10 Dec 2012 14:56:58 -0500
From: Yulin Huang <yulinhuang2007.gmail.com>
Subject: Re: [AMBER] For TI do corresponding same atoms in ligand
        pairs need to have the same charge
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CA+JH+ZY8YoXYvMXiML+uK-tjKw6R9HjXNAX2-jW1kCSXJxeNAg.mail.gmail.com>
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   Hi, Prof David Case,
   Thank you so much for your reply.   I am running a test now.  I do not
see how the charges transit from V0 to V1 with different lamdas.   Thus I
think "V1 may copy the charges from V0".
I just ran into this discussion during a committee meeting.
Yulin
On Mon, Dec 10, 2012 at 2:45 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Dec 10, 2012, Yulin Huang wrote:
>
> >  For states V0 and V1 unperturbed atoms (in other words, the same atoms
> > with the same coordinates), do they need to have exactly the same
> charges?
> > It seems that for V0 ->V1, V1 may copy the charges from V0 and for
> V1->V0,
> > V0 may copy the charges from V1.  This may lead to the wrong Hamiltonian.
>
> I think there is a nomenclature problem here:  TI has no conception of
> what is a "perturbed" or an "unperturbed" atom.  It simply computes the
> energy difference between the V0 and the V1 states of the entire system.
> I'd think of an atom that is changing its charge as being "perturbed", but
> the
> program doesn't keep any such list.
>
> I'd be curious to know what it is that makes you think that "V1 may copy
> the
> charges from V0".  As far as I can see, nothing like this takes place.
>
> Note also that with softcore, there *is* a distinction between
> "appearing/disappearing" atoms (which exist in one prmtop file but no the
> other) and common atoms (which exist in both prmtop files).  Common atoms
> don't need to have the same charges in the two endpoints.
>
> [Aside: "appearing/disappearing" is actually a bad choice of wording; such
> atoms are decoupled from their surroundings during the TI process--they
> don't
> actually disappear.]
>
> ...dac
>
>
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>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Tue Dec 11 2012 - 02:30:02 PST