Dear Jason, I gave a try and it’s simply wonderful.
However, I didn’t get the same E_pot_tot for the same system with U-B using
sander x gmx.
I took
---------------------------------
cat << EOF >| mdin
Single point
&cntrl
imin=0, maxcyc=0,
ntmin=2,
ntb=0,
igb=0,
cut=999,
//
EOF
cat << EOF >| SPE.mdp
define = -DFLEXIBLE
integrator = md
nsteps = 0
dt = 0.001
constraints = none
emtol = 10.0
emstep = 0.01
nstcomm = 1
ns_type = simple
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 1
pbc = no
nstlog = 1
nstenergy = 1
nstvout = 1
nstfout = 1
nstxtcout = 1
comm_mode = ANGULAR
continuation = yes
cutoff-scheme = group
EOF
cp $AMBERHOME/AmberTools/test/chamber/ala_ala_ala/inpcrd.save .
cp $AMBERHOME/AmberTools/test/chamber/ala_ala_ala/prmtop.save .
python2.7
import parmed as pmd
pmd.load_file('prmtop.save').save('gromacs.top')
exit()
# Gromacs 5.1
gmx grompp -f SPE.mdp -c prmtop.pdb -p gromacs.top -o gromacs.tpr
gmx mdrun -ntmpi 1 -v -deffnm gromacs
echo 1 2 3 4 5 6 7 8 9 10 11 12| gmx energy -f gromacs.edr
# EPot= 234.4 kJ/mol
# AT15
sander -O -i mdin -o mdout -p prmtop.save -c inpcrd.save
mv mdinfo prmtop.mdinfo
cat prmtop.mdinfo
# EPot= 39.1266 kcal/mol x 4.184 = 163.7057 kJ/mol
---------------------------------
For any other convencional system I tried, the SPE was nearly identical (as
well as with ACPYPE), but for this example from CHARMM, I didn’t get it.
Well, perhaps something going amiss in my ‘mdin’ and/or SPE.mdp file?
Many thanks,
Alan
PS. I am really glad to see how neat is this stuff working with python.
On 28 October 2015 at 14:08, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Oct 28, 2015 at 7:27 AM, Alan <alanwilter.gmail.com> wrote:
>
> > I found that now CHAMBER is part of ParmEd. Yet, still looking for a way
> to
> > generate Amber parm files with Charmm content.
> >
>
> ​The best way to do that is going to be with ParmEd -- this has gotten
> especially easier in recent versions on Github.
>
> The core data structure there -- called `Structure` -- that represents a
> FF-parametrized system has attributes with the various parameters and
> types. Once you instantiate one of those classes (or any subclass, like
> the GromacsTopologyFile or CharmmPsfFile), you can call instance.save("​
> something.parm7") and it will automatically convert to the Amber topology
> file format and save the file.
>
> If it has CHARMM-specific parameter types (namely arbitrary 1-4 L-J
> parameters, Urey-Bradley terms, or harmonic impropers), then the generated
> topology file will be the chamber-style.
>
> So for converting from a GROMACS topology specifying the CHARMM force field
> to an Amber prmtop is as simple as:
>
> import parmed as pmd
>
> pmd.load_file('gromacs.top').save('amber.parm7')
>
>
> Or converting the other way around:
>
> import parmed as pmd
>
> pmd.load_file('amber.parm7').save('gromacs.top')
>
> :). Inside the parmed interpreter, the only conversions supported are
> those *to* the Amber force field (the chamber and gromber actions).
>
> HTH,
> Jason
> ​
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
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Received on Thu Oct 29 2015 - 16:30:03 PDT
