Dear Amber users,
I have been trying to calculate free binding energy of my system. However,
there is an error as follows that I don't know how to solve
This is the output file
| Run on Wed Sep 14 15:57:36 ICT 2011
|Input file:
|--------------------------------------------------------------
|mmpbsa
|&general
| startframe=450, endframe=500, verbose=1,
| #entropy=1,
|/
|&pb
| istrng=0.100,
|/
|&nmode
|nmstartframe=450, nmendframe=500, nminterval=2,
|maxcyc=50000, drms=0.4,
|/
|--------------------------------------------------------------
|Solvated complex topology file: topol/complex.prmtop
|Complex topology file: topol/com.prmtop
|Receptor topology file: topol/rec.prmtop
|Ligand topology file: topol/ligand.prmtop
|Initial mdcrd(s): prod2.mdcrd
|
|Best guess for receptor mask: ":1-269"
|Best guess for ligand mask: ":270"
|Ligand residue name is "SUS"
|
|Calculations performed using 51 frames.
|NMODE calculations performed using -198 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
RADIUS_SET cannot be found in your prmtop files!
Error in computing entropy! Check nmode output files!
My mdcrd file contains 500 frames. Startframe of nmode is 450 and endframe
is 500. then the number of frames in nmode is supposed to be around 25 but
according to the output "NMODE calculations performed using -198 frames". I
do not understand at what step the error came from
And will the radius_set effect my results or not?
Thank you very much
--
Thank you very much
I am looking forward to hearing from you
Best wishes,
Nguyen Ngoc Hong Phuc
Email: phucnguyen20072.gmail.com
Mobile phone: +84 984620799
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 14 2011 - 03:00:03 PDT
