Hello sir,
I have successfully calculated DeltaG for my systems for namd generated
trajectories using CHAMBER in Parmed-Master and MMPBSA.py in Ambertools14.
For calculating overall free energy change, I need to remove vibrational
entropy part form the DeltaG calculated.
I tried calculating it from Nmode analysis available in ambertools.
SCRIPT: mmpbsa.in
&general
endframe=50, keep_files=2,
/
&nmode
nmstartframe=5, nmendframe=45,
nminterval=5, nmode_igb=1, nmode_istrng=0.1,
/
COMMAND:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp 2itp_mmpbsa.prmtop -cp
2itp_implicit.prmtop -rp 2itp_implicit_only-protein.prmtop -lp
2itp_implicit_only-ligand.prmtop -y newdcd.dcd > output_entropy.log
ERROR:
File "/home/vj/amber14/bin/MMPBSA.py", line 94, in <module>
app.loadcheck_prmtops()
File "/home/vj/amber14/bin/MMPBSA_mods/main.py", line 596, in
loadcheck_prmtops
raise MMPBSA_Error('CHAMBER prmtops cannot be used with NMODE')
MMPBSA_Error: CHAMBER prmtops cannot be used with NMODE
Exiting. All files have been retained.
Then I tried searching in amber archive were i got to see below link:
http://archive.ambermd.org/201408/0265.html
It has been mentioned that there is no *way to do NMODE for *
*a CHAMBER prmtop.since it was 8 months ago,i) Do we have any solution now
available to calculate nmode for CHAMBER prmtop..? ii) Is there any
alternative method to perform nmode analysis in ambertools..?*
*Thanks in advance*
*Regards*
*Vijay*
On Fri, Mar 13, 2015 at 4:36 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Fri, Mar 13, 2015, vijay kumar narsapuram wrote:
> >
> > 1) After going through amber manual I came across "kappa" keyword
> > k=(0.10806I)1/2,where "I" is ionic strength which is in [M].
> > is this keyword anyway helpful in calculating saltcon for my system.
>
> Various Amber programs are not completely consistent here. Basically,
> saltcon
> (ionic strength) and kappa are equilvalent variables: if you know one you
> can
> compute the other. Some programs ask for saltcon on input, and some for
> kappa.
>
> >
> > 2) In the paper they discussed about salt contribution in GB
> > theory,but I didn't get any of the formula related to saltconc
> > calculation.
>
> Please consult Ref. 122 in the Amber14 Reference Manual.
>
> ....dac
>
>
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Received on Sat Mar 28 2015 - 05:00:02 PDT
