Adk44: Created page with "Upper Level: GMIN (Under construction -- just posting a note on GMIN CHARMM data file and a set of input files for testing. 21 Jun 2011) The data file being used for CH..."

2019-05-10T17:07:23Z

Created page with "Upper Level: GMIN (Under construction -- just posting a note on GMIN CHARMM data file and a set of input files for testing. 21 Jun 2011) The data file being used for CH..."

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Upper Level: [[GMIN]]

(Under construction -- just posting a note on GMIN CHARMM data file and a set of input files for testing. 21 Jun 2011)

The data file being used for CHARMM GMIN runs so far included segments like

<pre>
! Generate PSF from sequence
READ SEQUence CARD
*
5
TYR GLY GLY PHE MET
GENErate FIRS NTER LAST CTER SETUp

</pre>

which effectively generates the topology file at every run. This is not very convenient since it makes the data file system dependent, unlike in the case of AMBER GMIN, for example. Alternatively, the psf file can be generated independently and then read in the GMIN data file:

<pre>
! READ psf from file
open unit 1 form read name input.psf
read psf card unit 1
close unit 1
</pre>

This approach is more in line with the usual way of setting up simulations based on CHARMM ff. The modified data file is

<pre>
comment DEBUG
SLOPPYCONV 0.001
TIGHTCONV 0.00001
ACCEPTRATIO 0.3
RINGROTSCALE 0.1
EDIFF 0.01
DUMPINT 100
UPDATES 800
MAXIT 10000 10000
TEMPERATURE 0.7
CHMD 5
STEPS 200 1.0
STEP 0.7 0.0
SAVE 10
CHARMMTYPE toph19_eef1_perm.inp param19_eef1_perm.inp
CHARMM
! Everything below the CHARMM line above is part of a CHARMM input file
set pardir "/home/csw34/svn/CHARMM31/toppar"

! BOMLev sets the level of warnings what do not cause the program to exit. -5 = very lax
BOMLev -5

! PRNLEV sets the ammount of output you get from CHARMM. 0 = small
PRNLEV 0

! Read standard topology and parameter files. These paths will need setting!
OPEN READ CARD UNIT 1 NAME @pardir/@top
READ RTF CARD UNIT 1
CLOSE UNIT 1

OPEN READ CARD UNIT 2 NAME @pardir/@par
READ PARAMETER CARD UNIT 2
CLOSE UNIT 2

! READ psf from file
open unit 1 form read name input.psf
read psf card unit 1
close unit 1

OPEN UNIT 20 NAME input.crd READ CARD
READ COOR UNIT 20 CARD FREE
CLOSE UNIT 20

! Build the internal coordinate tables
IC FILL PRESERVE
IC PARAMETERS
IC PURGE
IC BUILD

! Set up the EEF1 solvent model
eef1 setup temp 298.15 unit 93 name "/home/csw34/svn/CHARMM31/toppar/solvpar.inp"
update ctonnb 7. ctofnb 9. cutnb 15. group rdie
</pre>

I have tested it with met-enk input files:

1. '''input.crd'''

<pre>
48
1 1 TYR HT1 -3.81228 -2.32571 0.00000 1 1 0.00000
2 1 TYR HT2 -2.46994 -2.92617 0.84901 1 1 0.00000
3 1 TYR N -2.77563 -2.40912 0.00000 1 1 0.00000
4 1 TYR HT3 -2.46994 -2.92617 -0.84901 1 1 0.00000
5 1 TYR CA -2.18355 -1.08551 0.00000 1 1 0.00000
6 1 TYR CB -2.65921 -0.34765 1.24085 1 1 0.00000
7 1 TYR CG -2.09096 1.05900 1.33477 1 1 0.00000
8 1 TYR CD1 -2.74537 2.13959 0.77936 1 1 0.00000
9 1 TYR CE1 -2.20127 3.40356 0.88301 1 1 0.00000
10 1 TYR CD2 -0.89453 1.27775 1.98677 1 1 0.00000
11 1 TYR CE2 -0.37862 2.55484 2.07203 1 1 0.00000
12 1 TYR CZ -1.00276 3.58693 1.54207 1 1 0.00000
13 1 TYR OH -0.45866 4.85090 1.64572 1 1 0.00000
14 1 TYR HH 0.36919 4.80473 2.12958 1 1 0.00000
15 1 TYR C -0.66500 -1.15181 0.00000 1 1 0.00000
16 1 TYR O -0.06868 -2.22760 0.00000 1 1 0.00000
17 2 GLY N 0.00000 0.00000 0.00000 1 2 0.00000
18 2 GLY H -0.49000 0.84870 0.00000 1 2 0.00000
19 2 GLY CA 1.45000 0.00000 0.00000 1 2 0.00000
20 2 GLY C 2.00955 1.41326 0.00000 1 2 0.00000
21 2 GLY O 1.27275 2.39816 0.00000 1 2 0.00000
22 3 GLY N 3.33250 1.54997 0.00000 1 3 0.00000
23 3 GLY H 3.90715 0.75613 0.00000 1 3 0.00000
24 3 GLY CA 3.92458 2.87358 0.00000 1 3 0.00000
25 3 GLY C 5.44314 2.80728 0.00000 1 3 0.00000
26 3 GLY O 6.04133 1.73254 0.00000 1 3 0.00000
27 4 PHE N 6.10814 3.95910 0.00000 1 4 0.00000
28 4 PHE H 5.61814 4.80780 0.00000 1 4 0.00000
29 4 PHE CA 7.55814 3.95910 0.00000 1 4 0.00000
30 4 PHE CB 8.03745 3.22361 -1.24085 1 4 0.00000
31 4 PHE CG 9.55353 3.16795 -1.33477 1 4 0.00000
32 4 PHE CD1 10.27271 2.12935 -0.77936 1 4 0.00000
33 4 PHE CD2 10.24175 4.17077 -1.98677 1 4 0.00000
34 4 PHE CE1 11.64868 2.10990 -0.88301 1 4 0.00000
35 4 PHE CE2 11.61818 4.12023 -2.07203 1 4 0.00000
36 4 PHE CZ 12.30546 3.12906 -1.54207 1 4 0.00000
37 4 PHE C 8.11769 5.37236 0.00000 1 4 0.00000
38 4 PHE O 7.37917 6.35597 0.00000 1 4 0.00000
39 5 MET N 9.44064 5.50907 0.00000 1 5 0.00000
40 5 MET H 10.01529 4.71523 0.00000 1 5 0.00000
41 5 MET CA 10.03272 6.83268 0.00000 1 5 0.00000
42 5 MET CB 9.55707 7.57054 1.24085 1 5 0.00000
43 5 MET CG 10.12531 8.97719 1.33477 1 5 0.00000
44 5 MET SD 9.55891 9.85582 2.81236 1 5 0.00000
45 5 MET CE 10.40018 11.39527 2.57729 1 5 0.00000
46 5 MET C 11.55127 6.76638 0.00000 1 5 0.00000
47 5 MET OT1 12.07109 5.65162 0.00000 1 5 0.00000
48 5 MET OT2 12.16627 7.83159 0.00000 1 5 0.00000
</pre>

2. '''input.psf'''

<pre>
PSF CMAP CHEQ

2 !NTITLE
* NONE *
* DATE: 6/22/11 14:12:48 CREATED BY USER: ss2029

48 !NATOM
1 1 1 TYR HT1 2 0.450000 1.00800 0 0.00000 -0.301140E-02
2 1 1 TYR HT2 2 0.450000 1.00800 0 0.00000 -0.301140E-02
3 1 1 TYR N 40 -1.35000 14.0067 0 0.00000 -0.301140E-02
4 1 1 TYR HT3 2 0.450000 1.00800 0 0.00000 -0.301140E-02
5 1 1 TYR CA 12 0.00000 13.0190 0 0.00000 -0.301140E-02
6 1 1 TYR CB 13 0.00000 14.0270 0 0.00000 -0.301140E-02
7 1 1 TYR CG 92 0.00000 12.0110 0 0.00000 -0.301140E-02
8 1 1 TYR CD1 15 0.00000 13.0190 0 0.00000 -0.301140E-02
9 1 1 TYR CE1 15 0.00000 13.0190 0 0.00000 -0.301140E-02
10 1 1 TYR CD2 15 0.00000 13.0190 0 0.00000 -0.301140E-02
11 1 1 TYR CE2 15 0.00000 13.0190 0 0.00000 -0.301140E-02
12 1 1 TYR CZ 11 0.250000 12.0110 0 0.00000 -0.301140E-02
13 1 1 TYR OH 55 -0.650000 15.9994 0 0.00000 -0.301140E-02
14 1 1 TYR HH 1 0.400000 1.00800 0 0.00000 -0.301140E-02
15 1 1 TYR C 11 0.550000 12.0110 0 0.00000 -0.301140E-02
16 1 1 TYR O 51 -0.550000 15.9994 0 0.00000 -0.301140E-02
17 1 2 GLY N 38 -0.350000 14.0067 0 0.00000 -0.301140E-02
18 1 2 GLY H 1 0.250000 1.00800 0 0.00000 -0.301140E-02
19 1 2 GLY CA 13 0.100000 14.0270 0 0.00000 -0.301140E-02
20 1 2 GLY C 11 0.550000 12.0110 0 0.00000 -0.301140E-02
21 1 2 GLY O 51 -0.550000 15.9994 0 0.00000 -0.301140E-02
22 1 3 GLY N 38 -0.350000 14.0067 0 0.00000 -0.301140E-02
23 1 3 GLY H 1 0.250000 1.00800 0 0.00000 -0.301140E-02
24 1 3 GLY CA 13 0.100000 14.0270 0 0.00000 -0.301140E-02
25 1 3 GLY C 11 0.550000 12.0110 0 0.00000 -0.301140E-02
26 1 3 GLY O 51 -0.550000 15.9994 0 0.00000 -0.301140E-02
27 1 4 PHE N 38 -0.350000 14.0067 0 0.00000 -0.301140E-02
28 1 4 PHE H 1 0.250000 1.00800 0 0.00000 -0.301140E-02
29 1 4 PHE CA 12 0.100000 13.0190 0 0.00000 -0.301140E-02
30 1 4 PHE CB 13 0.00000 14.0270 0 0.00000 -0.301140E-02
31 1 4 PHE CG 92 0.00000 12.0110 0 0.00000 -0.301140E-02
32 1 4 PHE CD1 15 0.00000 13.0190 0 0.00000 -0.301140E-02
33 1 4 PHE CD2 15 0.00000 13.0190 0 0.00000 -0.301140E-02
34 1 4 PHE CE1 15 0.00000 13.0190 0 0.00000 -0.301140E-02
35 1 4 PHE CE2 15 0.00000 13.0190 0 0.00000 -0.301140E-02
36 1 4 PHE CZ 15 0.00000 13.0190 0 0.00000 -0.301140E-02
37 1 4 PHE C 11 0.550000 12.0110 0 0.00000 -0.301140E-02
38 1 4 PHE O 51 -0.550000 15.9994 0 0.00000 -0.301140E-02
39 1 5 MET N 38 -0.350000 14.0067 0 0.00000 -0.301140E-02
40 1 5 MET H 1 0.250000 1.00800 0 0.00000 -0.301140E-02
41 1 5 MET CA 12 0.100000 13.0190 0 0.00000 -0.301140E-02
42 1 5 MET CB 13 0.00000 14.0270 0 0.00000 -0.301140E-02
43 1 5 MET CG 13 0.600000E-01 14.0270 0 0.00000 -0.301140E-02
44 1 5 MET SD 81 -0.120000 32.0600 0 0.00000 -0.301140E-02
45 1 5 MET CE 14 0.600000E-01 15.0350 0 0.00000 -0.301140E-02
46 1 5 MET C 11 1.20000 12.0110 0 0.00000 -0.301140E-02
47 1 5 MET OT1 52 -0.600000 15.9994 0 0.00000 -0.301140E-02
48 1 5 MET OT2 52 -0.600000 15.9994 0 0.00000 -0.301140E-02

49 !NBOND: bonds
1 3 2 3 4 3 3 5
5 15 15 17 15 16 5 6
6 7 7 8 7 10 8 9
10 11 9 12 11 12 12 13
13 14 17 19 19 20 20 22
20 21 17 18 22 24 24 25
25 27 25 26 22 23 27 29
29 37 37 39 37 38 27 28
29 30 30 31 31 32 31 33
32 34 33 35 34 36 35 36
39 41 41 46 39 40 41 42
42 43 43 44 44 45 46 47
46 48
68 !NTHETA: angles
1 3 2 1 3 4 1 3 5
2 3 4 2 3 5 4 3 5
3 5 6 3 5 15 6 5 15
5 6 7 6 7 8 6 7 10
8 7 10 7 8 9 8 9 12
7 10 11 10 11 12 9 12 11
9 12 13 11 12 13 12 13 14
5 15 16 5 15 17 16 15 17
15 17 18 15 17 19 18 17 19
17 19 20 19 20 21 19 20 22
21 20 22 20 22 23 20 22 24
23 22 24 22 24 25 24 25 26
24 25 27 26 25 27 25 27 28
25 27 29 28 27 29 27 29 30
27 29 37 30 29 37 29 30 31
30 31 32 30 31 33 32 31 33
31 32 34 31 33 35 32 34 36
33 35 36 34 36 35 29 37 38
29 37 39 38 37 39 37 39 40
37 39 41 40 39 41 39 41 42
39 41 46 42 41 46 41 42 43
42 43 44 43 44 45 41 46 47
41 46 48 47 46 48

25 !NPHI: dihedrals
2 3 5 15 1 3 5 15
4 3 5 15 3 5 15 17
5 15 17 19 3 5 6 7
5 6 7 8 11 12 13 14
9 12 13 14 15 17 19 20
17 19 20 22 19 20 22 24
20 22 24 25 22 24 25 27
24 25 27 29 25 27 29 37
27 29 37 39 29 37 39 41
27 29 30 31 29 30 31 32
37 39 41 46 39 41 42 43
41 42 43 44 42 43 44 45
48 46 41 39

27 !NIMPHI: impropers
15 5 17 16 5 3 15 6
7 8 10 6 12 9 11 13
7 8 9 12 8 9 12 11
9 12 11 10 12 11 10 7
11 10 7 8 10 7 8 9
17 15 19 18 20 19 22 21
22 20 24 23 25 24 27 26
27 25 29 28 37 29 39 38
29 27 37 30 31 32 34 36
32 34 36 35 34 36 35 33
36 35 33 31 35 33 31 32
33 31 32 34 31 32 33 30
39 37 41 40 41 39 46 42
46 47 48 41

8 !NDON: donors
3 1 3 2 3 4 13 14
17 18 22 23 27 28 39 40

7 !NACC: acceptors
13 0 16 15 21 20 26 25
38 37 47 46 48 46

6 !NNB
12 11 10 36 35 34
0 0 0 0 0 0 1 2
3 3 3 3 3 3 3 3
3 3 3 3 3 3 3 3
3 3 3 3 3 3 4 5
6 6 6 6 6 6 6 6
6 6 6 6 6 6 6 6

18 0 !NGRP NST2
0 1 0 5 0 0 7 0 0
9 0 0 11 1 0 14 1 0
16 1 0 19 1 0 21 1 0
24 1 0 26 1 0 29 0 0
33 0 0 36 1 0 38 1 0
41 0 0 42 1 0 45 1 0

1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

0 0 !NUMLP NUMLPH

0 !NCRTERM: cross-terms
</pre>

3. '''chmd.par'''

<pre>
VERLET TIMESTEP 0.002 NSTEP 500 NPRINT 100 IPRFRQ 100 FIRSTT 500 FINALT 500 TWINDH 10.0 IEQFRQ 200 ICHECW 1 IASORS 0
IASVEL 1 INBFRQ 20
</pre>

Upper Level: [[GMIN]]

--[[User:Ss2029|Ss2029]] 17:46, 22 June 2011 (UTC)

Global optimization of biomolecules using CHARMM - Revision history

Adk44: Created page with "Upper Level: GMIN (Under construction -- just posting a note on GMIN CHARMM data file and a set of input files for testing. 21 Jun 2011) The data file being used for CH..."