xRe: [gmx-users] Normal mode analysis
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Thu Jul 24 09:22:01 CEST 2003
Hi Mark,
attaching is the topology file. You will able to do NMA by performing the
below commands, with the 3 input files: nm.mdp, xxx.gro,ala_gromo.top
Let me know if you need any help.
Phuong
>
> Thanks Nguyen for the normal mode example. I tried to get this to work,
> but was unable. I created a .tar file and attatched it. When I run
> grompp, it complains that I do not have a .top file.
>
> Thanks,
>
> Mark Fleharty
>
> On Tue, 24 Jun 2003, Nguyen Hoang Phuong wrote:
>
> > Hi,
> >
> > here are the simple commands used for NMA performed with Gromacs:
> >
> > grompp_d -v -f nm.mdp -c xxx.gro -o xxx.tpr -p xxx.top
> >
> > mdrun_d -s xxx.tpr -mtx nm.mtx
> >
> > g_nmeig_d -f nm.mtx -s xxx.tpr -o eigenvalue.xvg -v eigenvector.trr
> >
> > trjconv_d -f eigenvector.trr -s xxx.tpr -o eigenvector.gro
> >
> > At the end you will get the eigenvalues (related to normal mode
> > frequencies) stored in the file eigenvalue.xvg (in readable format)
> > and the eigenvectors in eigenvector.trr. If you want to read this
> > file, you have to convert it to readable format, using the last command.
> >
> > Here is the nm.mdp file:
> >
> > title = xxxx
> > cpp = /lib/cpp
> > include = -I../top
> > define =
> > integrator = nm
> > emtol = 0.000001
> > emstep = 0.000001
> > nstcgsteep = 1000
> > nsteps = 500000
> > nstxout = 50
> > xtc_grps = Protein
> > energygrps = Protein
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.
> > vdwtype = Shift
> > coulombtype = cut-off
> > rcoulomb = 0.
> > rvdw = 0.
> > pbc = no
> >
> > Here is xxx.gro file:
> >
> > Protein in water
> > 22
> > 1ALA N 1 1.004 1.392 0.821
> > 1ALA H1 2 1.025 1.300 0.785
> > 1ALA H2 3 0.922 1.427 0.774
> > 1ALA H3 4 1.081 1.454 0.799
> > 1ALA CA 5 0.981 1.389 0.967
> > 1ALA CB 6 0.884 1.276 1.000
> > 1ALA C 7 1.114 1.369 1.042
> > 1ALA O 8 1.209 1.317 0.985
> > 2ALA N 9 1.120 1.415 1.167
> > 2ALA H 10 1.040 1.454 1.216
> > 2ALA CA 11 1.245 1.414 1.246
> > 2ALA CB 12 1.282 1.558 1.284
> > 2ALA C 13 1.247 1.327 1.373
> > 2ALA O 14 1.147 1.309 1.442
> > 3ALA N 15 1.359 1.255 1.385
> > 3ALA H 16 1.398 1.214 1.302
> > 3ALA CA 17 1.404 1.194 1.513
> > 3ALA CB 18 1.423 1.043 1.493
> > 3ALA C 19 1.533 1.255 1.571
> > 3ALA OT 20 1.546 1.271 1.692
> > 3ALA O 21 1.635 1.294 1.489
> > 3ALA HO 22 1.701 1.342 1.552
> > 4.85000 4.85000 4.85000
> >
> >
> > Hope this help.
> >
> > Phuong
> >
> > >
> > >
> > > _______________________________________________
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> > >
> >
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> >
-------------- next part --------------
;
; File 'ttt1.top' was generated
; By user: phuong (523)
; On host: marge
; At date: Fri Mar 22 22:13:07 2002
;
; This is your topology file
; "The Wheels On the Bus Go Round and Round" (J. Richman)
;
; Include forcefield parameters
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NL 1 ALA N 1 0.129 14.0067 ; qtot 0.129
2 H 1 ALA H1 1 0.248 1.008 ; qtot 0.377
3 H 1 ALA H2 1 0.248 1.008 ; qtot 0.625
4 H 1 ALA H3 1 0.248 1.008 ; qtot 0.873
5 CH1 1 ALA CA 1 0.127 13.019 ; qtot 1
6 CH3 1 ALA CB 2 0 15.035 ; qtot 1
7 C 1 ALA C 3 0.38 12.011 ; qtot 1.38
8 O 1 ALA O 3 -0.38 15.9994 ; qtot 1
9 N 2 ALA N 4 -0.28 14.0067 ; qtot 0.72
10 H 2 ALA H 4 0.28 1.008 ; qtot 1
11 CH1 2 ALA CA 5 0 13.019 ; qtot 1
12 CH3 2 ALA CB 5 0 15.035 ; qtot 1
13 C 2 ALA C 6 0.38 12.011 ; qtot 1.38
14 O 2 ALA O 6 -0.38 15.9994 ; qtot 1
15 N 3 ALA N 7 -0.28 14.0067 ; qtot 0.72
16 H 3 ALA H 7 0.28 1.008 ; qtot 1
17 CH1 3 ALA CA 8 0 13.019 ; qtot 1
18 CH3 3 ALA CB 8 0 15.035 ; qtot 1
19 C 3 ALA C 9 0.53 12.011 ; qtot 1.53
20 O 3 ALA OT 9 -0.38 15.9994 ; qtot 1.15
21 OA 3 ALA O 9 -0.548 15.9994 ; qtot 0.602
22 H 3 ALA HO 9 0.398 1.008 ; qtot 1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_2
1 5 2 gb_20
5 6 2 gb_26
5 7 2 gb_26
7 8 2 gb_4
7 9 2 gb_9
9 10 2 gb_2
9 11 2 gb_20
11 12 2 gb_26
11 13 2 gb_26
13 14 2 gb_4
13 15 2 gb_9
15 16 2 gb_2
15 17 2 gb_20
17 18 2 gb_26
17 19 2 gb_26
19 20 2 gb_4
19 21 2 gb_12
21 22 2 gb_1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
2 6 1
2 7 1
3 6 1
3 7 1
4 6 1
4 7 1
5 10 1
5 11 1
6 8 1
6 9 1
7 12 1
7 13 1
8 10 1
8 11 1
9 14 1
9 15 1
10 12 1
10 13 1
11 16 1
11 17 1
12 14 1
12 15 1
13 18 1
13 19 1
14 16 1
14 17 1
15 20 1
15 21 1
16 18 1
16 19 1
17 22 1
18 20 1
18 21 1
20 22 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 2 ga_9
2 1 4 2 ga_9
2 1 5 2 ga_10
3 1 4 2 ga_9
3 1 5 2 ga_10
4 1 5 2 ga_10
1 5 6 2 ga_12
1 5 7 2 ga_12
6 5 7 2 ga_12
5 7 8 2 ga_29
5 7 9 2 ga_18
8 7 9 2 ga_32
7 9 10 2 ga_31
7 9 11 2 ga_30
10 9 11 2 ga_17
9 11 12 2 ga_12
9 11 13 2 ga_12
12 11 13 2 ga_12
11 13 14 2 ga_29
11 13 15 2 ga_18
14 13 15 2 ga_32
13 15 16 2 ga_31
13 15 17 2 ga_30
16 15 17 2 ga_17
15 17 18 2 ga_12
15 17 19 2 ga_12
18 17 19 2 ga_12
17 19 20 2 ga_29
17 19 21 2 ga_29
20 19 21 2 ga_32
19 21 22 2 ga_11
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 7 1 gd_14
1 5 7 9 1 gd_20
5 7 9 11 1 gd_4
7 9 11 13 1 gd_19
9 11 13 15 1 gd_20
11 13 15 17 1 gd_4
13 15 17 19 1 gd_19
15 17 19 21 1 gd_20
17 19 21 22 1 gd_3
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 1 7 6 2 gi_2
7 5 9 8 2 gi_1
9 7 11 10 2 gi_1
11 9 13 12 2 gi_2
13 11 15 14 2 gi_1
15 13 17 16 2 gi_1
17 15 19 18 2 gi_2
19 17 20 21 2 gi_1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
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