Dear AMBER user,
I'm doing a MMPBSA.py calculation on a ligand protein complex..The final file (FINAL_DECOMP_MMPBSA.dat) is empty. I have read similar problem but if my understanding was correct, it said that i need to mention the ligand as well in the print residue section. I have done so, i got the output this time, but i don't know why i should mention the ligand because the best guess mask has already mentioned the ligand correctly, here is my input:
Input file for running PB and GB
&general
startframe=1, endframe=2, verbose=1, netcdf=1
# entropy=1,
/
&gb
igb=2, saltcon=0.100, qm_residues="18-19"
/
&decomp
idecomp=1, print_res="18-19" (this gives empty output, but print_res="320, 18-19" gives the results below )
dec_verbose=1,
/
I have to other questions:
1-Can i use the ifqnt option eventhough my original trajectory is purely classical, i have read the manual and the AMBERtool but this was not clear...???.And if this is possible, do i need to include the ligand number as well or the script well correctly identify it to be included, and can this be paralleled or not....???
2-The output i got is messy, do i need a special program to open:
| Run on Wed May 16 10:01:30 2012
idecomp = 1: Per-residue decomp adding 1-4 interactions to Internal.
Energy Decomposition Analysis (All units kcal/mol): Generalized Born solvent
D,E,L,T,A,S,:
T,o,t,a,l, ,E,n,e,r,g,y, ,D,e,c,o,m,p,o,s,i,t,i,o,n,:
Residue,Location,Internal,,,van der Waals,,,Electrostatic,,,Polar Solvation,,,Non-Polar Solv.,,,TOTAL,,
,,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean
LEU 18,R LEU 18,0.0,0.0,0.0,-2.115,0.32,0.22627416998,-0.048,0.237,0.167584307141,0.606,0.033,0.0233345237792,-0.2487312,0.0210168,0.0148611217988,-1.8057312,0.0710168,0.0502164608582
GLY 19,R GLY 19,0.0,0.0,0.0,-0.2815,0.1265,0.0894490078201,0.1455,0.1245,0.0880347942577,-0.0415,0.0525,0.0371231060123,-0.0600228,0.0265788,0.0187940497158,-0.2375228,0.0810788,0.0573313692905
MOL 320,L MOL 1,0.0,0.0,0.0,-32.6475,0.7305,0.516541503657,-6.953,0.136,0.0961665222414,18.4435,0.5875,0.415425233947,-5.1337764,0.0346572,0.0245063411369,-26.2907764,0.3136572,0.221789133088
S,i,d,e,c,h,a,i,n, ,E,n,e,r,g,y, ,D,e,c,o,m,p,o,s,i,t,i,o,n,:
Residue,Location,Internal,,,van der Waals,,,Electrostatic,,,Polar Solvation,,,Non-Polar Solv.,,,TOTAL,,
,,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean
LEU 18,R LEU 18,0.0,0.0,0.0,-1.6795,0.1775,0.125511453661,0.1155,0.0575,0.0406586399182,-0.1365,0.0455,0.032173358544,-0.2001996,0.0067716,0.00478824427948,-1.9006996,0.1962716,0.138784979314
GLY 19,R GLY 19,0.0,0.0,0.0,-0.012,0.006,0.00424264068712,0.723,0.03,0.0212132034356,-0.612,0.038,0.0268700576851,-0.0552672,0.0218232,0.0154313327072,0.0437328,0.0521768,0.0368945691006
MOL 320,L MOL 1,0.0,0.0,0.0,-32.6475,0.7305,0.516541503657,-6.953,0.136,0.0961665222414,18.4435,0.5875,0.415425233947,-5.1337764,0.0346572,0.0245063411369,-26.2907764,0.3136572,0.221789133088
B,a,c,k,b,o,n,e, ,E,n,e,r,g,y, ,D,e,c,o,m,p,o,s,i,t,i,o,n,:
Residue,Location,Internal,,,van der Waals,,,Electrostatic,,,Polar Solvation,,,Non-Polar Solv.,,,TOTAL,,
,,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of Mean
LEU 18,R LEU 18,0.0,0.0,0.0,-0.436,0.143,0.10111626971,-0.163,0.295,0.20859650045,0.742,0.013,0.00919238815543,-0.0485388,0.0142524,0.0100779686882,0.0944612,0.1247476,0.0882098738967
GLY 19,R GLY 19,0.0,0.0,0.0,-0.2695,0.1335,0.0943987552884,-0.578,0.095,0.0671751442127,0.571,0.091,0.064346717088,-0.0047556,0.0047556,0.00336271700861,-0.2812556,0.1342556,0.0949330451723
MOL 320,L MOL 1,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
Thanks in advance
Marawan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 15 2012 - 17:30:03 PDT
