Thanks a lot Jason !
I am going to upgrade whole my Amber installation soon.
If anyone can comment below described differences in scee parameter
value during different stages of nmode analyses, please do it.
Best wishes,
Marek
Dne Wed, 21 Sep 2011 20:21:05 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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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>>
>
>
>
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Received on Wed Sep 21 2011 - 12:00:04 PDT
