Respected sir,
When i am running sander for my complex
minimization.It is generating following output.
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 03/07/2009 at 06:02:48
[-O]verwriting output
File Assignments:
| MDIN: minvac.in
| MDOUT:
DRUG0minvac.out
|INPCRD:
DRUG0.crd
| PARM:
DRUG0.top
|RESTRT:
DRUG0minvac.crd
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
in vacuo
minimization
&cntrl
imin =
1,
maxcyc =
1000,
ncyc =
200,
ntb =
0,
igb =
0,
cut =
12
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 49.070
| New format PARM file being parsed.
| Version = 1.000 Date = 03/07/09 Time = 06:02:30
NATOM = 2506 NTYPES = 15 NBONH = 1241 MBONA = 1297
NTHETH = 2798 MTHETA = 1764 NPHIH = 5299 MPHIA = 3375
NHPARM = 0 NPARM = 0 NNB = 13749 NRES = 160
NBONA = 1297 NTHETA = 1764 NPHIA = 3375 NUMBND = 52
NUMANG = 108 NPTRA = 43 NATYP = 38 NPHB = 0
IFBOX = 0 NMXRS = 39 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 160042
| Hollerith 15198
| Integer 249443
| Max Pairs 1443456
| nblistReal 30072
| nblist Int 1046806
| Total 12246 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1000, ncyc = 200, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 322 632 948 1270 1570 1879 2201
| 2506
Sum of charges from parm topology file = -1.00003006
| Running AMBER/MPI version on 8 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 66786
| TOTAL SIZE OF NONBOND LIST = 524450
Why it is not minimizing my complex.i do not know.my be the cavity size of
my complex is not as much as it has to be.please help me out
On Thu, Mar 12, 2009 at 10:07 PM, <rpaduri.chem.wayne.edu> wrote:
> Dear Bharat,
> Your "frcmod" file looks fine to me. The force constants and the bond
> lengths or
> the angles are in the right ranges. If you want to be absolutely sure you
> can
> energy minimize your molecule using any ab-initio methods and manually look
> at
> the bond lengths and angles. In my experience, the parameters you get from
> the
> antechamber are very well in the acceptable ranges. One thing I will
> suggest is
> to make sure your dihedrals are OK (which look fine to me).
> Good luck
> Sincerely
> Raviprasad Aduri
>
> Quoting bharat lakhani <lakhbharat.gmail.com>:
>
> > respected sir,
> > As you previous told me.I have done all the steps.I
> run
> > the antechamber to
> > find out which angle parameters are missing.
> >
> > *step 1*
> >
> > antechamber -i pencillinn.pdb -fi pdb -o pencillin.prepin -fo prepi -c
> bcc
> > -s 2
> >
> > *Step -2*
> >
> > parmchk -i pencillin.prepin -f prepi -o pencillin.frcmod
> >
> >
> > my pencillin.frcmod file generating these output
> >
> > *remark goes here
> > MASS
> >
> > BOND
> > n -cy 330.60 1.460 same as c3-n
> > cy-h2 326.40 1.100 same as c3-h2
> > cy-ss 225.80 1.821 same as c3-ss
> >
> > ANGLE
> > c -n -cy 63.900 121.350 same as c -n -c3
> > n -cy-h1 49.800 109.320 same as h1-c3-n
> > n -cy-c 66.700 111.560 same as c -c3-n
> > hn-n -cy 46.000 116.780 same as c3-n -hn
> > cy-c -n 67.619 101.125 Calculated with empirical approach
> > cy-cy-h2 44.800 115.140 same as cy-cy-hc
> > cy-cy-ss 61.100 112.690 same as c3-c3-ss
> > h1-cy-c 45.700 113.850 same as c -cy-hc
> > n -cy-h2 50.000 108.310 same as h2-c3-n
> > n -cy-ss 63.716 111.415 Calculated with empirical approach
> > cy-n -c3 64.000 112.620 same as c3-n -c3
> > cy-ss-c3 60.600 99.920 same as c3-ss-c3
> > h2-cy-ss 42.300 109.750 same as h2-c3-ss
> >
> > DIHE
> > cy-cy-ss-c3 1 0.333 0.000 3.000 same as X
> > -c3-ss-X
> > n -cy-ss-c3 1 0.333 0.000 3.000 same as X
> > -c3-ss-X
> > h2-cy-ss-c3 1 0.333 0.000 3.000 same as X
> > -c3-ss-X
> >
> > IMPROPER
> >
> > NONBON
> >
> > *
> > So these are the parameters which are missing in my complex.Are they
> > correct.
> > or i have to validate these parameters can i incorporate these
> > parameters.What will be the my next step:
> >
> >
> > On Mon, Mar 9, 2009 at 3:35 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> > > Dear bharat lakhani,
> > >
> > > Sir,i dont know how to run QM can you tell me how can i run QM for
> these
> > >> ligands if you have some tutorial regarding this QM please let me know
> > >>
> > >
> > > ok I better understand your needs now: You need (i) to derive the
> > > atomic charges, (ii) to determine the force field (FF) atom types, and
> > > (iii) find the missing FF parameters (if any) for your molecules:
> > >
> > > (i) To get the charges, you can follow different approaches.
> > > You could use the following plan:
> > > - You get optimized structures by quantum mechanics (QM).
> > > You need a QM program for that: Among the numerous possibilities:
> > > Gaussian, PC-GAMESS or GAMESS-US (the last twos are provided at no
> > > cost).
> > > - You compute molecular electrostatic potential (MEP).
> > > - You fit the charges to the MEP.
> > > You can use the R.E.D. tools or Antechamber for that.
> > >
> > > If you decide to use the R.E.D. tools, Ante_R.E.D. will generate for
> > > you inputs for the geometry optimization step, and R.E.D. will allow
> > > you to compute the charges for all your molecules in a single
> > > multi-molecule approach.
> > >
> > > (ii) you need to decide which FF you want to use. If you decide to use
> > > GAFF, Antechamber will generate the FF atom types for GAFF and find
> > > the missing FF parameters. For other FF, you will have to do the job
> > > manually.
> > >
> > > (iii) you use LEaP to load the FF libraries and generate the
> > > prmtop/prmcrd files. LEaP will tell you which FF parameter is missing.
> > >
> > > I hope this helps. A lot of work... I suggest you to proceed step by
> > > step taking a small molecule as a model first.
> > >
> > > regards, Francois
> > >
> > >
> > >
> > > On Mon, Mar 9, 2009 at 1:40 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> > >>
> > >> Dear bharat lakhani,
> > >>>
> > >>> As You told me previously that in which
> sturctures u
> > >>>
> > >>>> have sulphru and chlorine.i mentioned those structures previously
> and
> > >>>> now
> > >>>> i
> > >>>> am again sending you.But i did get any reply from your side.
> > >>>>
> > >>>>
> > >>> Yes sorry. This is difficult to answer you because one needs to work
> on
> > >>> the
> > >>> structures to see the error messages & missing FF parameters.
> > >>>
> > >>> please help me
> > >>>
> > >>>> out sir.In my structures there are sulfa drugs like
> > >>>> sulfanilamide,pencillin
> > >>>> g,sulfathiazole,pencillin v,Sulfamethoxazole,Pencillin V and the
> > >>>> structure
> > >>>> which have chlorine Chlorpropamide,Tigecycline,Aureomycin I am
> looking
> > >>>> for
> > >>>> these above force field parameters
> > >>>>
> > >>>>
> > >>> Did you already get the atomic charges for those molecules ?
> > >>> You did not talk about the charges; only about FF parameters...
> > >>>
> > >>> Did you load your structures in LEaP, and what are the missing FF
> > >>> parameters ?
> > >>>
> > >>> I think you need to generate your own charges + the missing FF
> > >>> parameters.
> > >>> * optimized by QM all your structures
> > >>> * run R.E.D. or Antechamber to get the charges // FF parameters
> > >>> * run LEaP to save the prmtop/prmcrd files for all your structures.
> > >>>
> > >>> I am not sure I help you a lot here...
> > >>>
> > >>> regards, Francois
> > >>>
> > >>
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
>
>
>
>
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Received on Sun Mar 15 2009 - 01:16:06 PDT
