On Sat, Mar 28, 2015 at 7:47 AM, vijay kumar narsapuram <
nvijay1991.gmail.com> wrote:
> 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..?
No. And this support is not planned.
> ii) Is there any
> alternative method to perform nmode analysis in ambertools..?*
>
You can try the quasi-harmonic approximation. See the relevant literature
(citation should be in the AmberTools manual, and is definitely in the
MMPBSA.py citation).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Mar 28 2015 - 12:00:03 PDT
