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
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> 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.
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Received on Wed Feb 10 2016 - 04:30:03 PST
