.....
.....
.....
Type
core name of the output files
:
!!!Your Project name is test: Default is test
Do
you have a topology file (y/n)
?
!!!Default Value set was No:n
Do
you have a template to extract constraints from
?
!!!Default Value set was YES: y
Name
of the seq. align. file (master alignment)
?
!!!Alignment File must be supplied by Users: seq.aln
Enter
the name of the pdb file
?
!!!PDB File must be supplied by Users: 1RER.pdb
Enter
interval (deg) for PSI/PHI (default 10)
:
!!!Default Value set was 10:10
Enter
interval (deg) for OMEGA (default 5)
:
!!!Default Value set was 5:5
Number
of distance constraints per atom (default 15)
:
!!!Default Value set was 15:15
Enter
threshold between upper and lower limits (default
0.5):
!!!Default Value set was 0.5:.5
Do
you like to specify fragments (y/n)
?
!!!Default Value set was n:n
STOP
0 statement executed
Do
you have another template to extract constraints from (y/n)
?
!!!Default Value set was n:n
*******************************
!!!--- EXDIS COMPLETED ----!!!
*******************************
Do
you have disulphide bonds in the target
?
!!! Disulphide Bond Y/N:y
No.
of SS bonds
?
!!! Disulphide Bond are 8
!!! Disulphide Bonds are 49,114
!!! Disulphide Bonds are 62,94
!!! Disulphide Bonds are 63,96
!!! Disulphide Bonds are 68,78
!!! Disulphide Bonds are 259,271
!!! Disulphide Bonds are 301,376
!!! Disulphide Bonds are 306,380
!!! Disulphide Bonds are 328,370
Do
you want to run DIAMOD
?
!!! Running DIAMOD: y
How
many structures do you want to generate
?
!!! Number of Structure You want to Generate 1
Enter
how many cycles of SECODG do you want to run (1 if no SECODG)
?
!!! Cycles of SECODG=1
*******************************
!!!--- EXECUTING DIAMOD ----!!!
*******************************
DIAMOD:
DIstance geometry Algorithm for MODelling
(UNIX version 2.2, double precision)
Output
result file (res, default: diana.res):
Input
library file (lib, default:
/home/people/negi/MPACK1.0//library/diana.lib):
Input
sequence file (seq):
Input
stereospecific assignments file (ssa, default: none):
Input
upper distance limits file (upl, default: none):
Input
lower distance limits file (lol, default: none):
Input
angle constraints file (aco, default: none):
Input
minimization parameters file (min, default: none):
Check
gradient numerically (default: n)?
Input
structure file or number of structures and seed (ang, default: 1 3771):
Output
cutoffs: f, upper/lower/vdW/angle, fraction (default: 100 3*0.2 5 100):
Output
modified upper distance limits file (upl, default: none):
Output
modified lower distance limits file (lol, default: none):
Target
function cutoffs to eliminate bad structures (default: none):
Output
overview file (ovw, default: diana.ovw):
Options:
vdW violations, H-bonds, RMSDs, connectivities (default: ynnn)?
Output
angle files (ang, default: none):
Output
coordinate files (cor, default: none):
Output
angle constraint file (aco, default: none):
Angle
constraint cutoffs: f/res., no. of struct., width (default: 0.2 10 270):
Output
corrected upl file (upl, default: none):
fraction
of upl viol: fcont (default: 0.5 0.9):
Output
corrected lol file (lol, default: none):
fraction
of lol viol: fextent (default: 0.5 1.1):
Structure
1:
lev upper
lower vdw angle
target funct. |grad| #up #f stop
# act # act #
act # act begin
end end
1 0 0 0
0 0 3389 1161417 25
2.19 0.15 3.2E-3 0 192 gradtl
2 1 0 0
0 0 9507 2241417 88
3.15 0.89 2.8E-3 5 228 gradtl
3 2 172 2 185 2 10332
2371417 91 3.93 0.89 2.8E-3
6 263 gradtl
4 4 995 54 1007 57 10735 2951417
142 18.74 0.95 3.1E-3 14 955 gradtl
5 6 1639 137 1651 177 10866 3461417 219
8.33 1.03 6.4E-3 16 1242 flat
6 11 2803 363 2814 439 11246 4181417 253 22.91
1.21 1.8E-2 24 1779 flat
.....
.....
.....
*******************************
!!!--- HAPPY MODELLING ----!!!
*******************************
_________________________________________________________________________________________________________________________________
************************************************************************
MPACKbeta v 2.0 3D MODELING PACKAGE FOR
PROTEINS
************************************************************************
Computational Biology Group, SCSB, UTMB, GALVESTON
READ INSTRUCTIONS BEFORE USE REPORT ERRORS TO
ssnegi@utmb.edu or werner@newton.utmb.edu
http://129.109.59.109/mpack/
Modified and Updated By Surendra S Negi and Werner Braun
06/12/2004
Originally Design and Developed by Venkatrajan Mathura and Werner Braun
Please Check your alignment and PDB file before Running MPACKbeta
Example of MPACKbeta Running with
Two PDB Templates
Here MPACK uses two different sequence alignments their template PDB
************************************************************************
Type
core name of the output files
:
!!!Your Project name is test: Default is test
Do
you have a topology file (y/n)
?
!!!Default Value set was No:n
Do
you have a template to extract constraints from
?
!!!Default Value set was YES: y
Name
of the seq. align. file (master alignment)
?
!!!Alignment File must be supplied by Users: 8faba.aln
Enter
the name of the pdb file
?
!!!PDB File must be supplied by Users: y.pdb
Enter
interval (deg) for PSI/PHI (default 10)
:
!!!Default Value set was 10:10
Enter
interval (deg) for OMEGA (default 5)
:
!!!Default Value set was 5:5
Number
of distance constraints per atom (default 15)
:
!!!Default Value set was 15:15
Enter
threshold between upper and lower limits (default
0.5):
!!!Default Value set was 0.5:.5
Do
you like to specify fragments (y/n)
?
!!!Default Value set was n:y
###############################################################################################################################
Define fragments of model sequence that will be used to generate
dihedral and distance constraints.
Format: residue_number <--space--> residue_number Type "0 0" to
take entire sequence into account,
or to end fragment definition Enter pairs of numbers:1st
###############################################################################################################################
!!!Default Value set was :0 0
STOP
0 statement executed
Do
you have another template to extract constraints from (y/n)
?
!!!Default Value set was n:y
Enter
the starting residue number of the target sequence in the alignment
file? !!!check your
residue number and type its number:1
Enter
the name of the sequence alignment file
?
!!!Added Fragment Alignment file:8fabb.aln
Enter
the name of the pdb file
?
!!!Added Fragment PDB file: 1CU4.pdb
Enter
interval (deg) for PSI/PHI (default 10)
:
!!!Default Value set was 10
Enter
interval (deg) for OMEGA (default 5)
:
!!!Default Value set was 5: 5
Number
of distance constraints per atom (default 15)
:
!!!Default Value set was 15:15
Enter
threshold between upper and lower limits (default
0.5):
!!!Default Value set was 0.5: .5
??Do
you like to specify fragments (y/n)
?
!!! Specify Another Fragments Y/N:n
STOP
0 statement executed
---???Do
you have another template to extract constraints from (y/n) ?
*******************************
!!!--- EXDIS COMPLETED ----!!!
*******************************
Do
you have disulphide bonds in the target
?
!!! Disulphide Bond Y/N:n
Do
you want to run DIAMOD ? y
!!! Running DIAMOD: y
How
many structures do you want to generate
?
!!! Number of Structure You want to Generate 1
Enter
how many cycles of SECODG do you want to run (1 if no SECODG)
?
!!! Cycles of SECODG=1
*******************************
!!!--- EXECUTING DIAMOD ----!!!
*******************************
DIAMOD:
DIstance geometry Algorithm for MODelling
(UNIX version 2.2, double precision)
Output
result file (res, default: diana.res):
Input
library file (lib, default:
/home/people/negi/MPACK1.0//library/diana.lib):
Input
sequence file (seq):
Input
stereospecific assignments file (ssa, default: none):
Input
upper distance limits file (upl, default: none):
Input
lower distance limits file (lol, default: none):
Input
angle constraints file (aco, default: none):
Input
minimization parameters file (min, default: none):
Check
gradient numerically (default: n)?
Input
structure file or number of structures and seed (ang, default: 1 3771):
Output
cutoffs: f, upper/lower/vdW/angle, fraction (default: 100 3*0.2 5 100):
Output
modified upper distance limits file (upl, default: none):
Output
modified lower distance limits file (lol, default: none):
Target
function cutoffs to eliminate bad structures (default: none):
Output
overview file (ovw, default: diana.ovw):
Options:
vdW violations, H-bonds, RMSDs, connectivities (default: ynnn)?
Output
angle files (ang, default: none):
Output
coordinate files (cor, default: none):
Output
angle constraint file (aco, default: none):
Angle
constraint cutoffs: f/res., no. of struct., width (default: 0.2 10 270):
Output
corrected upl file (upl, default: none):
fraction
of upl viol: fcont (default: 0.5 0.9):
Output
corrected lol file (lol, default: none):
fraction
of lol viol: fextent (default: 0.5 1.1):
Structure
1:
lev upper
lower vdw angle
target funct. |grad| #up #f stop
# act # act #
act # act begin
end end
1 0 0 0
0 0 581 18 273 9
139.48 2.13 2.5E-3 0 167 gradtl
2 1 0 0
0 0 1654 33 273 20
4.04 2.23 3.0E-3 3 104 gradtl
3 2 360 35 383 24 1829
42 273 42 4.22 2.60 3.0E-3
6 229 gradtl
4 4 1190 156 1212 136 1992 53 273
54 10.59 3.09 3.1E-3 10 548 gradtl
5 6 1876 278 1898 292 2090 69 273
62 9.54 3.58 3.1E-3 16 1063 gradtl
6 11 3365 541 3387 693 2203 77 273 70
10.83 4.56 1.2E-2 13 1101 flat
7 16 4693 929 47151190 2394 86 273 72
17.28 5.57 0.13 19 1525 flat
8 21 57491176 57691561 2565 102 273 68
7.84 6.24 0.11 26 2000 maxit
9 31 72841358 73041788 2562 102 273 72
7.99 6.56 0.12 11 1081 flat
10 42 77981471 78181930 2546 103 273 76
6.76 6.71 0.21 11 1001 flat
11 47 78261472 78461940 2548 104 273 77
6.73 6.73 2.2E-2 11 1001 flat
12 52 78261480 78461941 2543 104 273 75
6.73 6.69 2.2E-2 12 1001 flat
13 57 78261478 78461946 2544 105 273 78
6.69 6.69 1.8E-2 11 1001 flat
14 60 78261687 78461963 7812 130 273 62
21.25 11.61 0.91 21 2000 maxit
15 61 78261768 78462054 7813 124 273 60
15.21 15.07 0.35 11 1001 flat
16 62 78261844 78462083 7822 123 273 55
21.94 21.75 0.78 11 1001 flat
17 63 78261971 78462099 7811 116 273 57
31.64 31.45 1.61 11 1001 flat
*******************************
!!!--- HAPPY MODELLING ----!!!
*******************************