The only programs capable of printing 1-4 scaling parameters in the topology
file are tleap from a fully-patched AmberTools 1.5 (which is the
*recommended* way by the glycam folks to create a topology file) or sleap
from AmberTools 1.4 or greater (although I think there are known issues
regarding sleap and glycam).
HTH,
Jason
On Wed, Sep 21, 2011 at 1:56 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 21 2011 - 11:30:04 PDT
