the answer to this depends strongly on your goals and what you plan to do.
If you want to compare the linear and cyclized peptides, and you use a
highly optimized protein force field for one and GAFF for the other, it
will be very difficult to know if the differences are because you used
different force fields or because of the covalent structure. Isolation of
variables is crucial here.
You don't need parameters for the entire peptide, just for the modified Asp
and modified Lys. Then you could use the bond command in leap to create the
covalent link. You probably need to develop new partial charges, assign
appropriate atom types (the existing ones for Asp and Lys will not be
correct), and then develop new dihedral parameters for these atom types if
any are missing. What approximations you make during these steps depends on
your project goals.
On Wed, Feb 10, 2016 at 7:12 AM, Mohammed Khaled Tumbi <
khaledtumbi.gmail.com> wrote:
> Dear Dr. Simmerling:
> I had a thought of using antechamber to calculate charges.
> But not sure about validity of GAFF forcefield for a peptide molecule which
> is 13 amino acid length.
> Any suggestions how to proceed?/.
> Regards.
>
>
> On Tue, 9 Feb 2016 at 20:00 <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. Getting and keeping ACPYPE updated (Alan)
> > 2. Is the Force Constant in the Parm**.dat file derived from a
> > mass-weighted Hessian (Thomas Collier)
> > 3. Re: Is the Force Constant in the Parm**.dat file derived from
> > a mass-weighted Hessian (Jason Swails)
> > 4. Re: Is the Force Constant in the Parm**.dat file derived from
> > a mass-weighted Hessian (Nash, Anthony)
> > 5. Parameter for Aspartic Acid-Lysine Cyclic peptide
> > (Mohammed Khaled Tumbi)
> > 6. Re: Parameter for Aspartic Acid-Lysine Cyclic peptide
> > (Carlos Simmerling)
> > 7. Parameter for Aspartic Acid-Lysine Cyclic peptide
> > (Mohammed Khaled Tumbi)
> > 8. Re: Question about AmberTools14/15 installation (A kS)
> > 9. Re: Question about AmberTools14/15 installation (Jason Swails)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 9 Feb 2016 11:33:03 +0000
> > From: Alan <alanwilter.gmail.com>
> > Subject: [AMBER] Getting and keeping ACPYPE updated
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEznbz=5OxscV3x_eZOVJUYNus5FN=
> > VkdZgN6rJAUzkKyM5Cvw.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi everyone,
> >
> > Many thanks for those who helped for, used or are interested in ACPYPE.
> >
> > Since Google Code is now archived and, at University of Cambridge, it has
> > moved), the right way to get it now is by:
> >
> > svn checkout
> > http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype
> > acpype
> >
> > Thanks,
> >
> > Alan
> >
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > Senior Bioinformatician, UniProt
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > United Kingdom
> > Tel: +44 (0)1223 494588
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 9 Feb 2016 11:56:15 +0000
> > From: Thomas Collier <t.collier.12.ucl.ac.uk>
> > Subject: [AMBER] Is the Force Constant in the Parm**.dat file derived
> > from a mass-weighted Hessian
> > To: <amber.ambermd.org>
> > Message-ID: <56B9D3DF.2030509.ucl.ac.uk>
> > Content-Type: text/plain; charset="utf-8"; format=flowed
> >
> > Dear All,
> >
> > I am currently trying to derive force constants for a new residue in
> > amber. I have derived my force constants, but they are significantly
> > different to analogous atom types already present in amber. However if I
> > do not mass weight the Hessian, the values obtained are close to those
> > present for analogous atom types in the parm13.dat file.
> >
> > My question is are the values for the force constants present in Amber
> > parm**.dat files derived from the mass weighted Hessian? Or is the
> > atomic mass taken into account later, when running LeaP?
> >
> > Thanks in Advance,
> >
> > Thomas Collier
> > -----------------------------------
> > Final Year PhD Student
> > Department of Chemistry
> > University College London
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 9 Feb 2016 07:39:37 -0500
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Is the Force Constant in the Parm**.dat file
> > derived from a mass-weighted Hessian
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEk9e3r165RhcXQ1LCgC+qK6fMDGvqbdFfwtXFe=
> > uoGcGmQMuw.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Tue, Feb 9, 2016 at 6:56 AM, Thomas Collier <t.collier.12.ucl.ac.uk>
> > wrote:
> >
> > > Dear All,
> > >
> > > I am currently trying to derive force constants for a new residue in
> > > amber. I have derived my force constants, but they are significantly
> > > different to analogous atom types already present in amber. However if
> I
> > > do not mass weight the Hessian, the values obtained are close to those
> > > present for analogous atom types in the parm13.dat file.
> > >
> > > My question is are the values for the force constants present in Amber
> > > parm**.dat files derived from the mass weighted Hessian? Or is the
> > > atomic mass taken into account later, when running LeaP?
> > >
> >
> > ?I believe it is taken from the mass-weighted Hessian (isn't that the
> only
> > way the units work out correctly?). Did you account for the fact that
> > Amber "force constants" are not really force constants, but rather
> > half-force constants? That is, the m-w Hessian should give you k such
> that
> > U=1/2*k*(x-xeq)^2, whereas the force constants in the Amber parameter
> files
> > correspond to U=k*(x-xeq)^2. So they should be half as large (give or
> > take) as the values you derive from QM frequency calculations.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 9 Feb 2016 13:34:52 +0000
> > From: "Nash, Anthony" <a.nash.ucl.ac.uk>
> > Subject: Re: [AMBER] Is the Force Constant in the Parm**.dat file
> > derived from a mass-weighted Hessian
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <D2DF99E0.B8EF%uccaja0.ucl.ac.uk>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Jason,
> >
> > We have taken into account the 1/2 factor that you mentioned. With
> regards
> > to the mass weighting, we are deriving down from Gaussian?s Hessian
> > (Hartree/bohr_radius^2) into the final kcal/(mol.ang^2) as required for
> > Amber. However, we?re seeing discrepancies through the literature. Some
> > publications are showing derived force constants which are within the
> same
> > kind of kcal/mol.Ang^2 you would expect for Amber (e.g., 200-500 range),
> > but others are showing bond stretch values in the region of 20-100.
> > Neither set of publications mention mass weighting. Whilst testing our
> own
> > methodology, we can reproduce the former value range *without* mass
> > weighting, and the later *with* mass weighting.
> >
> > It is interesting that you introduced the idea of the mass weighted units
> > - I?m not quite clear how the units would end up being cancelled out from
> > the final calculation to derive force constants.
> >
> > Thanks
> > Anthony
> >
> >
> > Dr Anthony Nash
> > Department of Chemistry
> > University College London
> >
> >
> >
> >
> >
> > On 09/02/2016 12:39, "Jason Swails" <jason.swails.gmail.com> wrote:
> >
> > >On Tue, Feb 9, 2016 at 6:56 AM, Thomas Collier <t.collier.12.ucl.ac.uk>
> > >wrote:
> > >
> > >> Dear All,
> > >>
> > >> I am currently trying to derive force constants for a new residue in
> > >> amber. I have derived my force constants, but they are significantly
> > >> different to analogous atom types already present in amber. However
> if I
> > >> do not mass weight the Hessian, the values obtained are close to those
> > >> present for analogous atom types in the parm13.dat file.
> > >>
> > >> My question is are the values for the force constants present in Amber
> > >> parm**.dat files derived from the mass weighted Hessian? Or is the
> > >> atomic mass taken into account later, when running LeaP?
> > >>
> > >
> > >?I believe it is taken from the mass-weighted Hessian (isn't that the
> only
> > >way the units work out correctly?). Did you account for the fact that
> > >Amber "force constants" are not really force constants, but rather
> > >half-force constants? That is, the m-w Hessian should give you k such
> > >that
> > >U=1/2*k*(x-xeq)^2, whereas the force constants in the Amber parameter
> > >files
> > >correspond to U=k*(x-xeq)^2. So they should be half as large (give or
> > >take) as the values you derive from QM frequency calculations.
> > >
> > >HTH,
> > >Jason
> > >
> > >--
> > >Jason M. Swails
> > >BioMaPS,
> > >Rutgers University
> > >Postdoctoral Researcher
> > >_______________________________________________
> > >AMBER mailing list
> > >AMBER.ambermd.org
> > >http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 09 Feb 2016 14:44:18 +0000
> > From: Mohammed Khaled Tumbi <khaledtumbi.gmail.com>
> > Subject: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide
> > To: amber <amber.ambermd.org>
> > Message-ID:
> > <CAEJ44H=BEQYfJzq2+1jJ+BDHMX=
> > 3R2yuZVLSMWRnHmGcoYA-SQ.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear All:
> > I am trying to simulate a large cyclic peptide in complex with protein
> > using FF14SB.
> > To get cyclic peptide, I made a amide bond between side chains of Asp and
> > Lys. (Carboxylic group of Aspartic Acid with Amino group of Lysine).
> >
> > After that I change atom types for corresponding O,N,C, H to atom types
> > similar to peptide bond. (is this correct ?).
> >
> > But as expected I getting error in leap for missing parameters.
> >
> > Could not find bond parameter for: C8 - N
> > Checking for angle parameters.
> > Could not find angle parameter: C - N - C8
> > Could not find angle parameter: HP - C8 - N
> > Could not find angle parameter: HP - C8 - N
> > Could not find angle parameter: C8 - N - H
> > Could not find angle parameter: C8 - C8 - N
> >
> > ** No torsion terms for C-N-C8-C8
> > ** No torsion terms for C-N-C8-HP
> > ** No torsion terms for C-N-C8-HP
> > ** No torsion terms for HP-C8-N-H
> > ** No torsion terms for HP-C8-N-H
> > ** No torsion terms for C8-C8-N-H
> >
> > Can any one suggest something.
> > Best Regard.
> > --
> > --------------------------------------------------------
> > Tumbi Mohammed Khaled.
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 9 Feb 2016 09:55:11 -0500
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Subject: Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> > CAGk3s-SbepGQK80cJeJnMD3V2VVv0nCGHKtFx-QuhqvPjVdPZw.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > That's a start but there is much more to it. How did you derive the
> partial
> > charges for the cyclized part? There will be additional steps after that
> > too.
> > On Feb 9, 2016 9:44 AM, "Mohammed Khaled Tumbi" <khaledtumbi.gmail.com>
> > wrote:
> >
> > > Dear All:
> > > I am trying to simulate a large cyclic peptide in complex with protein
> > > using FF14SB.
> > > To get cyclic peptide, I made a amide bond between side chains of Asp
> and
> > > Lys. (Carboxylic group of Aspartic Acid with Amino group of Lysine).
> > >
> > > After that I change atom types for corresponding O,N,C, H to atom types
> > > similar to peptide bond. (is this correct ?).
> > >
> > > But as expected I getting error in leap for missing parameters.
> > >
> > > Could not find bond parameter for: C8 - N
> > > Checking for angle parameters.
> > > Could not find angle parameter: C - N - C8
> > > Could not find angle parameter: HP - C8 - N
> > > Could not find angle parameter: HP - C8 - N
> > > Could not find angle parameter: C8 - N - H
> > > Could not find angle parameter: C8 - C8 - N
> > >
> > > ** No torsion terms for C-N-C8-C8
> > > ** No torsion terms for C-N-C8-HP
> > > ** No torsion terms for C-N-C8-HP
> > > ** No torsion terms for HP-C8-N-H
> > > ** No torsion terms for HP-C8-N-H
> > > ** No torsion terms for C8-C8-N-H
> > >
> > > Can any one suggest something.
> > > Best Regard.
> > > --
> > > --------------------------------------------------------
> > > Tumbi Mohammed Khaled.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Tue, 09 Feb 2016 15:05:26 +0000
> > From: Mohammed Khaled Tumbi <khaledtumbi.gmail.com>
> > Subject: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide
> > To: amber <amber.ambermd.org>
> > Message-ID:
> > <
> > CAEJ44HmDigWXq4yWKhC0RCmbzfn4U6u29qfm8MLGq25gMyMGAw.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear All:
> > I am trying to simulate a large cyclic peptide in complex with protein
> > using FF14SB.
> > To get cyclic peptide, I made a amide bond between side chains of Asp and
> > Lys. (Carboxylic group of Aspartic Acid with Amino group of Lysine).
> >
> > After that I change atom types for corresponding O,N,C, H to atom types
> > similar to peptide bond. (is this correct ?).
> >
> > But as expected I getting error in leap for missing parameters.
> >
> > Could not find bond parameter for: C8 - N
> > Checking for angle parameters.
> > Could not find angle parameter: C - N - C8
> > Could not find angle parameter: HP - C8 - N
> > Could not find angle parameter: HP - C8 - N
> > Could not find angle parameter: C8 - N - H
> > Could not find angle parameter: C8 - C8 - N
> >
> > ** No torsion terms for C-N-C8-C8
> > ** No torsion terms for C-N-C8-HP
> > ** No torsion terms for C-N-C8-HP
> > ** No torsion terms for HP-C8-N-H
> > ** No torsion terms for HP-C8-N-H
> > ** No torsion terms for C8-C8-N-H
> >
> > Can any one suggest something.
> > Best Regard.
> > --
> > --------------------------------------------------------
> > Tumbi Mohammed Khaled.
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Wed, 10 Feb 2016 00:40:03 +0530
> > From: A kS <aks25121986.gmail.com>
> > Subject: Re: [AMBER] Question about AmberTools14/15 installation
> > To: AMBER Mailing List <amber.ambermd.org>, jason.swails.gmail.com
> > Message-ID:
> > <CAO6J-3Gcz4AgDpr+=nCuU=RY=
> > zgDpuy1y6iSD6E9nCWOM2jkyA.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Respected Sir,
> >
> > Thank you very much for your reply.The installation logic is now quite
> > clear to me. Just to make sure that I understood it properly I used an
> > example of AmberTools14/15:
> >
> > 1. export AMBERHOME = 'pwd' : *will set the 'pwd' as AMBERHOME*
> > 2. doing ./configure gnu: *will configure the application*
> > 3. export amber.sh : *will *
> > * (a) export AMBERHOME and *
> > * (b) check if LD_LIBRARY_PATH (for example) is set or not, if *NOT*
> > then it will set LD_LIBRARY_PATH="${AMBERHOME}/lib", *else* it
> > will append the **"${AMBERHOME}/lib" to the
> > LD_LIBRARY_PATH.*
> > 4. make install : install the Amber
> > 5. export "source $AMBERHOME/amber.sh" >> ~/.bashrc" :
> > *will add* **exactly** this "source $AMBERHOME/amber.sh" line to
> > .bashrc. *So if I open .bashrc I will find that line written in the
> > .bashrc.* *This will ensure that when ever I login the login shell source
> > the respective amber.sh file.*
> >
> >
> >
> ***********************************************************************************************
> > I have one more technical question and I hope you will not mind If I
> > discussed :
> >
> > I want to install, 1. Amber12 coupled with AmberTools13, 2.AmberTools14
> and
> > 3. AmberTools15 one by one in a system:
> >
> > 1. *For Amber12+AmberTools13*
> >
> > export AMBERHOME ='pwd'
> > ./configure gnu
> > make install
> > the add these lines to .bashrc
> > export AMBERHOME=/home/aditya/applications/amber12
> > export PATH=$AMBERHOME/bin:$PATH
> >
> > 2. *Then for AmberTools14*
> >
> > *comment out following lines in .bashrc*
> > #export AMBERHOME=/home/aditya/applications/amber12
> > #export PATH=$AMBERHOME/bin:$PATH
> > *then do:*
> > export AMBERHOME='pwd'
> > ./configure gnu
> > source amber.sh
> > make install
> > echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
> > This will add /home/user/ambertools14/amber.sh to .bashrc
> >
> > 3.*Then for AmberTools15*
> >
> > *Comment out following lines in .bashrc*
> > #export AMBERHOME=/home/aditya/applications/amber12
> > #export PATH=$AMBERHOME/bin:$PATH
> > #source /home/user/ambertool14/amber.sh
> > *the repeat the same as above*
> >
> > *Now to use only Amber12 and AmberTools13:*
> >
> > Changing the following lines in .bashrc
> >
> > export AMBERHOME=/home/aditya/applications/amber12
> > export PATH=$AMBERHOME/bin:$PATH
> > #source /home/user/ambertool14/amber.sh
> > #source /home/user/ambertool15/amber.sh
> >
> > *Now to use only AmberTools14*
> >
> > Changing the following lines in .bashrc
> >
> > #export AMBERHOME=/home/aditya/applications/amber12
> > #export PATH=$AMBERHOME/bin:$PATH
> > source /home/user/ambertool14/amber.sh
> > #source /home/user/ambertool15/amber.sh
> >
> >
> > Sorry to bother you for this repeatedly. Looking forward for your reply.
> >
> > Regards
> >
> > On Mon, Feb 8, 2016 at 6:45 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Mon, Feb 8, 2016 at 3:15 AM, A kS <aks25121986.gmail.com> wrote:
> > >
> > > > Dear AMBER user,
> > > >
> > > > I am new to AMBER. I am trying to install the AmberTools14 and
> > > AmberTools15
> > > > in Ubuntu 12.04 64 bit system. After reading the Jason Swails
> > > installation
> > > > instruction and doing some trials with both the AmberTools I found
> that
> > > the
> > > > amber.sh file have these lines :
> > > >
> > > >
> > > >
> > > >
> > >
> >
> *********************************************************************************************************in
> > > > AmberTools14:*
> > > >
> > > > if [ -z "${LD_LIBRARY_PATH}" ]; then
> > > > export LD_LIBRARY_PATH="${AMBERHOME}/lib"
> > > > else
> > > > export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${AMBERHOME}/lib"
> > > > fi
> > > >
> > > > *in AmberTools15*:
> > > >
> > > > if [ -z "$PYTHONPATH" ]; then
> > > > export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
> > > > else
> > > > export
> > > > PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
> > > > fi
> > > > if [ -z "${LD_LIBRARY_PATH}" ]; then
> > > > export LD_LIBRARY_PATH="${AMBERHOME}/lib"
> > > > else
> > > > export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
> > > > fi
> > > >
> > > >
> > > >
> > >
> >
> *******************************************************************************************************************
> > > >
> > > > *Instruction says that after doing ./configure we can do "source
> > > amber.sh"
> > > > and after make install "echo "source $AMBERHOME/amber.sh" >>
> > ~/.bashrc"*
> > > >
> > > > My problems are:
> > > >
> > > > 1. I am unable to clearly understand the meaning of that "if else
> > loop".
> > > > What I found out that, if [ -z "something" ] means: if "something" is
> > > > absent then do task1 else task2. So when I source that amber.sh in
> > > terminal
> > > > how exactly it add all paths to my .bashrc file, at least the syntax.
> > > >
> > >
> > > ?There are two scenarios that can happen with an environment variable
> > that
> > > specifies a path -- it can either be set or it can be *not* set. The
> > "if [
> > > -z $VARIABLE ]" is true if the variable is *not* set. So what that
> logic
> > > is doing is testing to see if LD_LIBRARY_PATH or PYTHONPATH (which are
> > > environment variables controlling where the ld loader looks for shared
> > > libraries at runtime and where Python looks for modules at runtime,
> > > respectively) are set. If they are *not* set, they get set to the
> values
> > > that Amber needs. If they *are* set, we don't want to overwrite their
> > > original values, so the values that Amber needs are prepended to the
> > list.
> > > The main difference between what that script does and the lines in your
> > > .bashrc file:
> > >
> > > export LD_LIBRARY_PATH=${AMBERHOME}/lib:$LD_LIBRARY_PATH
> > >
> > > is that if LD_LIBRARY_PATH is *not* set at that time, the resulting
> value
> > > is "/path/to/amber14:", with a trailing :. It doesn't ruin things,
> but I
> > > don't like stuff like that which is why I implemented that logic in
> > > amber.sh and amber.csh
> > > ?
> > >
> > > > 2. Doing "*echo "source $AMBERHOME/amber.sh" >> ~/.bashrc*" will add
> > the
> > > > "source $AMBERHOME/amber.sh" line to .bashrc and how it will help to
> > run
> > > > AMBER in future.
> > > >
> > >
> > > ?If your main shell is bash, then login shells source the commands in
> > your
> > > .bashrc (or .profile/.bash_profile) file. So that command will put the
> > > line "source /path/to/amber14/amber.sh" in your .bashrc file, making
> sure
> > > that when you start a new shell that file is sourced. ("sourcing" a
> file
> > > is the logical equivalent of copying the contents of the sourced file
> at
> > > the point where it is sourced).?
> > > ??
> > >
> > > 3. I learned little bit of old style of adding path to .bashrc. So I
> add
> > > > these lines to .bashrc for all the AmberTools
> > > >
> > > >
> > > >
> > >
> >
> *********************************************************************************
> > > > export AMBERHOME=/home/a/application/ambertools15
> > > > #export AMBERHOME=/home/a/application/ambertools14
> > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
> > > > export PATH=$AMBERHOME/bin:$PATH
> > > > export DO_PARALLEL='mpiexec.hydra -n 8'
> > > >
> > > >
> > >
> >
> **************************************************************************************
> > > >
> > >
> > > ?This is *exactly* what "source $AMBERHOME/amber.sh" would do, except
> it
> > > would do a better job. First of all, the fact that you didn't add the
> > > PYTHONPATH part means that Python programs (like MMPBSA.py) won't work.
> > > Second, DO_PARALLEL is *not* an environment variable that Amber
> requires.
> > > It's only used for *parallel* tests, and could cause problems when
> trying
> > > to run serial tests. You should remove the declaration of that
> > environment
> > > variable and only set it when it is specifically needed.
> > >
> > > I highly recommend running the above-mentioned command:
> > >
> > > echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
> > >
> > > and removing the lines you mentioned above from your .bashrc file.
> > >
> > > so that whenever I need any of the amberttools (i know its silly cause
> > now
> > > > AmberTools15 have all the features of its previous version) I just
> > > comment
> > > > the other AMBERHOME containing line.
> > > > Is it correct one??
> > > >
> > >
> > > ?I'm not exactly sure what you're asking here. Changes to your .bashrc
> > > file will only affect terminals that you open *after* saving those
> > > changes. If you change your .bashrc, it won't affect any shells that
> are
> > > already running. So just "commenting out" a line in your .bashrc?
> > >
> > > ?won't affect terminal windows that are already open.
> > >
> > > If you have the amber.sh file sourced in your .bashrc, you will be able
> > to
> > > use Amber in any terminal you start.
> > >
> > > HTH,
> > > Jason
> > > ?
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Tue, 9 Feb 2016 14:18:41 -0500
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Question about AmberTools14/15 installation
> > To: A kS <aks25121986.gmail.com>
> > Cc: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> > CAEk9e3qDKOw3Upfp89riJWfbYa_gzCUMQLnO+QfMJktsL2HoyA.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Tue, Feb 9, 2016 at 2:10 PM, A kS <aks25121986.gmail.com> wrote:
> >
> > > Respected Sir,
> > >
> > > Thank you very much for your reply.The installation logic is now quite
> > > clear to me. Just to make sure that I understood it properly I used an
> > > example of AmberTools14/15:
> > >
> > > 1. export AMBERHOME = 'pwd' : *will set the 'pwd' as AMBERHOME*
> > > 2. doing ./configure gnu: *will configure the application*
> > > 3. export amber.sh : *will *
> > >
> >
> > ?This should be "source amber.sh".
> > ?
> >
> >
> > > * (a) export AMBERHOME and *
> > > * (b) check if LD_LIBRARY_PATH (for example) is set or not, if
> *NOT*
> > > then it will set LD_LIBRARY_PATH="${AMBERHOME}/lib", *else*
> it
> > > will append the **"${AMBERHOME}/lib" to the
> > > LD_LIBRARY_PATH.*
> > > 4. make install : install the Amber
> > > 5. export "source $AMBERHOME/amber.sh" >> ~/.bashrc" :
> > > *will add* **exactly** this "source $AMBERHOME/amber.sh" line to
> > > .bashrc. *So if I open .bashrc I will find that line written in the
> > > .bashrc.* *This will ensure that when ever I login the login shell
> source
> > > the respective amber.sh file.*
> > >
> > >
> > >
> >
> ***********************************************************************************************
> > > I have one more technical question and I hope you will not mind If I
> > > discussed :
> > >
> > > I want to install, 1. Amber12 coupled with AmberTools13, 2.AmberTools14
> > > and 3. AmberTools15 one by one in a system:
> > >
> >
> > ?There is no point to installing both AmberTools 14 and AmberTools 15 --
> > they both offer exactly the same programs and are both free. The only
> > difference is that AmberTools 14 is no longer supported.
> > ?
> >
> >
> > >
> > > 1. *For Amber12+AmberTools13*
> > >
> > > export AMBERHOME ='pwd'
> > > ./configure gnu
> > > make install
> > > the add these lines to .bashrc
> > > export AMBERHOME=/home/aditya/applications/amber12
> > > export PATH=$AMBERHOME/bin:$PATH
> > >
> > > 2. *Then for AmberTools14*
> > >
> > > *comment out following lines in .bashrc*
> > > #export AMBERHOME=/home/aditya/applications/amber12
> > > #export PATH=$AMBERHOME/bin:$PATH
> > > *then do:*
> > > export AMBERHOME='pwd'
> > > ./configure gnu
> > > source amber.sh
> > > make install
> > > echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
> > > This will add /home/user/ambertools14/amber.sh to .bashrc
> > >
> > > 3.*Then for AmberTools15*
> > >
> > > *Comment out following lines in .bashrc*
> > > #export AMBERHOME=/home/aditya/applications/amber12
> > > #export PATH=$AMBERHOME/bin:$PATH
> > > #source /home/user/ambertool14/amber.sh
> > > *the repeat the same as above*
> > >
> > > *Now to use only Amber12 and AmberTools13:*
> > >
> > > Changing the following lines in .bashrc
> > >
> > > export AMBERHOME=/home/aditya/applications/amber12
> > > export PATH=$AMBERHOME/bin:$PATH
> > > #source /home/user/ambertool14/amber.sh
> > > #source /home/user/ambertool15/amber.sh
> > >
> > > *Now to use only AmberTools14*
> > >
> > > Changing the following lines in .bashrc
> > >
> > > #export AMBERHOME=/home/aditya/applications/amber12
> > > #export PATH=$AMBERHOME/bin:$PATH
> > > source /home/user/ambertool14/amber.sh
> > > #source /home/user/ambertool15/amber.sh
> > >
> >
> > ?This sounds about right. You can also use pmemd from Amber 12 and
> > AmberTools 15 by following instructions here:
> > http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > End of AMBER Digest, Vol 1481, Issue 1
> > **************************************
> >
> --
> --------------------------------------------------------
> Tumbi Mohammed Khaled.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 10 2016 - 05:00:04 PST
