Thank you for your help. I proceeded as you suggested and managed to generate topology files using AmberTools16.
I also used AmberTools16 for structure minimisation, heat and density equilibration using sander.MPI
When I reverted to the Amber12 installation to use pmemd.MPI I encountered the following problem
mpirun -np 4 pmemd.MPI -O -i equil_1ns.in -o equil_1ns.out -p complex_solv.prmtop -c density.rst -r equil_1ns.rst -x equil_1ns.nc -ref density.rst
[proxy:0:0.Georges-Mac-Pro.local] HYDU_create_process (utils/launch/launch.c:75): execvp error on file pmemd.MPI (No such file or directory)
[proxy:0:0.Georges-Mac-Pro.local] HYDU_create_process (utils/launch/launch.c:75): execvp error on file pmemd.MPI (No such file or directory)
Etc………..
Yet my environment seems to be OK
# MacPorts Installer addition on 2017-03-31_at_18:37:23: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin/Users/gtzotzos/Programs/amber12/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:$PATH
# Finished adapting your PATH environment variable for use with MacPorts.
export AMBERHOME=/Users/gtzotzos/Programs/amber12
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib
source /Users/gtzotzos/Programs/amber12/amber.sh
I tested the parallel installation of Amber12 and encountered no problems
export AMBERHOME=/Users/gtzotzos/Programs/amber12
export DO_PARALLEL='mpirun -np 2’
make test.parallel
All tests pass
I’d appreciate any suggestions on how to resolve this problem
Thank you in advance
George
> On 8 Aug 2017, at 21:55, David A Case <david.case.rutgers.edu> wrote:
>
> On Tue, Aug 08, 2017, George Tzotzos wrote:
>
>>
>> saveamberparm DIMER complex_solv.prmtop complex_solv.inpcrd
>>
>> Checking Unit.
>> Building topology.
>> Building atom parameters.
>> For atom: .R<Na+ 254>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
>> For atom: .R<Na+ 255>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
>> ……………………………………………………………………………etc
>> For atom: .R<Na+ 271>.A<Na+ 1> Could not find vdW (or other) parameters for type: Na+
>> Parameter file was not saved.
>>
>> Can’t figure this out as I did source leaprc.ff14SB
>
> But you never loaded the parameters for the ions. In old versions of Amber,
> you must use loadAmberParams to choose the force field parameters for the ions
> that go along with your chosen water model.
>
> I strongly recommend upgrading to AmberTools17 (although the relevant changes
> were also present in AmberTools16 -- we haven't supported a "leaprc.ff14SB"
> in either of the past two releases.)
>
> With AmberTools17, there are leaprc.protein.*, leaprc.DNA.*, leaprc.RNA.*
> and leaprc.water.* files. By choosing a water model, you automatically get
> the corresponding ion files that go with that water model.
>
> A couple notes:
>
> 1. you can keep pmemd from Amber14 and still use everything else from
> AmberTools17. (pmemd is the only program not in AmberTools). Just set
> your AMBERHOME variable to the amber16 tree: the pmemd program doesn't need
> or use the AMBERHOME variable. (Of course, you can also upgrade to Amber16
> if you wish.)
>
> 2. Going forward, use "NA" for sodium, not "Na+". The former is the PDB
> standard; the latter is a non-standard name that should be phased out.
>
> ....dac
>
>
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Received on Wed Aug 09 2017 - 08:30:02 PDT
