Hello all,
I am trying to get LES with restraints working (want to use addles output with makeDIST_RST) and not having success...
just to verify which addles I am running:
which addles: /usr/local/amber10/exe/addles
Command: addles<addles.in>addles.out
addles.in:
file rprm name=(model8.prmtop) read
file wprm name=(lesparm) wovr
file rcrd name=(model8.crd) read
file wcrd name=(lescrd) wovr
action
spac numc=5 pick #prt 1 157 done
*EOD
addles.out:
AMBER8 Module: addles
set up Locally Enhanced Sampling topology
add_les> file rprm name=(model8.prmtop) read
The following unit number was assigned 26
| New format PARM file being parsed.
| Version = 1.000 Date = 02/01/10 Time = 14:22:36
Checking topology sizes against compiled limits
Checking topology sizes against compiled limits
add_les> file wprm name=(lesparm) wovr
The following unit number was assigned 27
add_les> file rcrd name=(model8.crd) read
The following unit number was assigned 28
urcrd: 28
Coordinates only from unit 28
Reading coordinates from input file
add_les> file wcrd name=(lescrd) wovr
The following unit number was assigned 29
add_les> action
add_les> spac numc=5 pick #mon 1 7 done
picking from 2010 particles
Picked 126 particles
Making 5 copies
there were 2010 particles; currently 2514 particles
there were 884 nbonh bonds, now there are 1144
there were 1201 nbona bonds, now there are 1445
there were 0 nbper bonds, now there are 0
there were 2014 ntheth angles, now there are 2586
there were 1728 ntheta angles, now there are 2044
there were 0 ngper angles, now there are 0
there were 3980 nphih torsions, now there are 5096
there were 3600 nphia torsions, now there are 4356
there were 0 ndper torsions, now there are 0
processing exclusion list
finished creating LES subspace
Checking topology sizes against compiled limits
add_les> *EOD
Finished reading subspace definitions.
Looking for unique atom and covalent types
3 1 1.09000000000000 68.0000000000000
2 1.09000000000000 340.000000000000
5 3 1.01000000000000 86.8000000000000
4 1.01000000000000 434.000000000000
7 5 0.960000000000000 110.600000000000
6 0.960000000000000 553.000000000000
8 7 1.09000000000000 68.0000000000000
8 1.09000000000000 340.000000000000
11 9 1.01000000000000 86.8000000000000
10 1.01000000000000 434.000000000000
13 11 1.09000000000000 68.0000000000000
12 1.09000000000000 340.000000000000
14 13 1.01000000000000 86.8000000000000
14 1.01000000000000 434.000000000000
17 15 1.08000000000000 367.000000000000
18 16 1.01000000000000 434.000000000000
20 17 1.08000000000000 367.000000000000
26 18 1.08000000000000 367.000000000000
49 19 1.08000000000000 367.000000000000
53 20 1.09000000000000 340.000000000000
55 21 1.09000000000000 340.000000000000
59 22 1.08000000000000 367.000000000000
61 23 1.08000000000000 367.000000000000
69 24 1.08000000000000 367.000000000000
bond with hydrogen: 24
There were 70 bond types, now there are 86
There were 163 angle types, now there are 197
There were 73 dihedral types, now there are 102
There were 17 atom typesNow there are 27
MAX # ATOMS IN A SINGLE RESIDUE = 120
ATOM origpt
Writing coordinates to output file
Successful completion of ADDLES
However, if I want to use makeDIST_RST, I need the correlations of old atom numbers to new atom numbers, which does not appear in the ouput file.
I ran the test LES sim in Amber 10 - this did not have the appropriate output either (had no new atom to old atom numbering matches).
I am in the process of bugfixing/recompiling, but am skeptical as to whether this will fix this problem.
Thanks in advance!
Jamie
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Received on Wed Feb 03 2010 - 12:30:03 PST
