Hello,
I am trying to calculate the binding energy of a receptor and a ligand
using the MMPBSA.py module. Here is my input mmpbsa.in file:
---------------------------------
Input file for running PB and GB in serial
&general
receptor_mask=':1-468:509-510', ligand_mask=':469-508',
endframe=20, verbose=2,
/
&gb
igb=2, saltcon=0.100
/
---------------------------------
And this is the command i used:
---------------------------------
MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop
-rp receptor.prmtop -lp ligand.prmtop -y test.mdcrd
---------------------------------
Here is the output i get:
---------------------------------
Warning: Input error! "keep_files=2" is an invalid option.
ptraj found! Using /data/apps/amber9_mvapich2//exe/ptraj
1568,1579c1331,1337
sander found! Using /data/apps/amber9_mvapich2//exe/sander (serial only!)
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
modified Bondi radii (mbondi)
Preparing trajectories with ptraj...
20 frames were read in and processed by ptraj for use in calculation.
Starting sander calls
Starting gb calculation...
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
-rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
mdinfo -radii radii]
Consult the manual for additional options.
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
-rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
mdinfo -radii radii]
Consult the manual for additional options.
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
-rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
mdinfo -radii radii]
Consult the manual for additional options.
Error: Sander error! GB mdout file not created.
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
---------------------------------
I have checked the output files generated by ptraj during the steps
before the sander run, and they are all as expected. The problem seems
to be with sander not recognising the -y flag. I am using amber9,
compiled using all the bugfixes. The amber9 manual mentions the -y
flag, so why is sander complaining that it is an unknown flag? The
sander program runs perfectly for a "regular MD" run, where one uses
the -c flag for an inpcrd file as input. Any pointers appreciated.
Thanks,
arvind
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Received on Mon Feb 15 2010 - 07:00:02 PST
