Dear all,
I have question about SCEE parameter.
I recently did MM/PBSA analyses of my system using mm_pbsa.pl script .
I set variable VERBOSE to 1 to have possibilities to check all parameters
in intermediate files.
For calculation of entropy I used nmode program. What surprised me here
was that in output files
for sander minimization (sandmin*.out) generated during the calculation I
found different value for
scee parameter than in case of output files for normal mode calculation
(nmode*.out).
Below are sandmin*.in and nmode*.in files and relevant parts of both
output files mentioned above.
As you can see in sandmin*.out is scee=1.2 while in case of nmode*.out
there is scee=2.0.
To be frank I would assume the same value of scee parameter during all
stages of the normal mode calculation,
more likely value 1.2 as in my system GAFF (scee=1.2), ff99bsc0
(scee=1.2), Glycam_06 (scee=1) forcefields are used.
So if nmode scee default value scee=2.0 ? should be changed in my case,
how to do it ? I did not find any information
about setting this parameter using standard mm_pbsa.pl input file. I guess
it could be done by writing this parameter
directly in nmode*.in file which is by default created by mm_pbsa.pl
script. If I am right, how is then possible to correctly run
mm_pbsa.pl with "by hand" created sandmin*.in and nmode*.in files instead
of standard mm_pbsa input file ?
I would like also to know why sander printed "Note: 1-4 EEL scale factors
were NOT found in the topology file.".
Is it because I am using several ffs which differ in scee (scnb)
parameters and for my input files using tleap ( AmberTools 1.4 )
instead of sleap ?
Thanks a lot for any relevant comment !
Best wishes,
Marek
********** sandmin*.in ***************
File generated by mm_pbsa.pl
&cntrl
ntxo = 0,
ntf = 1, ntb = 0,
dielc = 4,
cut = 99.0, nsnb = 99999,
imin = 1, maxcyc = 100000,
ncyc = 0, drms = 0.1
&end
&ewald
eedmeth= 5,
&end
********** nmode*.in ***************
File generated by mm_pbsa.pl
&data
ntx = 0,
ntrun = 1, nvect = 0,
drms = 1,
dielc = 4.0, idiel = 0,
idecomp= 0
&end
END
********* Here is the relevant part of sandmin*.out file ***************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 09/21/2011 at 09:16:51
[-O]verwriting output
File Assignments:
| MDIN: sanmin_rec.in
| MDOUT: sanmin_rec.49.out
|INPCRD: ../0_snaps/snap_rec.crd.49
| PARM: ../prmtop/rec.prmtop
|RESTRT: sanmin_rec.49.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
File generated by mm_pbsa.pl
&cntrl
ntxo = 0,
ntf = 1, ntb = 0,
dielc = 4,
cut = 99.0, nsnb = 99999,
imin = 1, maxcyc = 100000,
ncyc = 0, drms = 0.1
&end
&ewald
eedmeth= 5,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 69.584
| New format PARM file being parsed.
| Version = 1.000 Date = 08/18/11 Time = 10:43:28
NATOM = 9444 NTYPES = 16 NBONH = 5086 MBONA = 4565
NTHETH = 11759 MTHETA = 6277 NPHIH = 19874 MPHIA = 11858
NHPARM = 0 NPARM = 0 NNB = 54866 NRES = 570
NBONA = 4565 NTHETA = 6277 NPHIA = 11858 NUMBND = 55
NUMANG = 117 NPTRA = 66 NATYP = 34 NPHB = 0
IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 570343
| Hollerith 28904
| Integer 1847559
| Max Pairs 44589846
| nblistReal 113328
| nblist Int 11956716
| Total 233556 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
*********** Here is the relevant part of nmode*.out file
**********************
*******************************************************
Initiate the NMODE module of AMBER 8
*******************************************************
File generated by mm_pbsa.pl
ntrun maxcyc ibelly drms
1 100 0 0.10E+01
rcut scnb scee dielc idiel
99.00000 2.00000 2.00000 4.00000 0
nsave dfpred bdwnhl smx emx alpha ndiag
20 0.01000 0.10000 0.08000 0.30000 0.80000 10
ipol = 0
i3bod = 0
idecomp = 0
nvect = 0
Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 08/18/11 Time = 10:43:28
PARM file has the title:
Total memory required : 1204540903 real words
Total memory required : 45152989 integer words
Total memory required : 28907 4-character words
Maximum nonbond pairs 44589845
Duplicated 0 dihedrals
Duplicated 0 dihedrals
Getting coordinates from file with title:
################################################
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Received on Wed Sep 21 2011 - 11:30:03 PDT
