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grompp error
- Rajat Desikan
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12 years 3 months ago #880
by Rajat Desikan
grompp error was created by Rajat Desikan
Hi
I want to use polarizable water with a membrane protein (POPC+Protein) system I built the system according to the protocols. However, i am getting a error while running grompp..
Fatal error:
Molecule type 'PW' contains no atoms
Here is my .itp file for the system (Protein_A.itp is separate and is generated with martinize.py)
; topology section
;;;;;; POLARIZABLE WATER, POPC PARAMETERS, IONS
[ moleculetype ]
; molname nrexcl
PW 1
NA+ 1
POPC 1
[ atoms ]
;id type resnr residue atom cgnr charge
1 Q0 1 POPC NC3 1 1.0
2 Qa 1 POPC PO4 2 -1.0
3 Na 1 POPC GL1 3 0
4 Na 1 POPC GL2 4 0
5 C1 1 POPC C1A 5 0
6 C1 1 POPC C2A 6 0
7 C1 1 POPC C3A 7 0
8 C1 1 POPC C4A 8 0
9 C1 1 POPC C1B 9 0
10 C1 1 POPC C2B 10 0
11 C3 1 POPC D3B 11 0
12 C1 1 POPC C4B 12 0
13 C1 1 POPC C5B 13 0
14 POL 1 PW W 1 0
15 D 1 PW WP 1 0.46
16 D 1 PW WM 1 -0.46
17 Qd 1 ION NA+ 1 1.0
#ifndef EM
[constraints]
; i j funct length
14 15 1 0.14
14 16 1 0.14
#else[bonds]
; i j funct length force const.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
14 15 1 0.14 50000
14 16 1 0.14 50000
#endif
[angles]
; i j k funct angle fc
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 120.0 45.0
11 12 13 2 180.0 25.0
15 14 16 2 0.0 4.2
[exclusions]
14 15 16
15 16
; for minimization purposes replace constraints by stiff bonds:
My .top file is as follows:
#include "martini_combined.itp"
#include "Protein_A_mod.itp"
[ system ]
; name
Martini system from 1.pdb
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
POPC 286
PW 61655 (originally it was 20555 W molecules, now I have counted WP and WM too)
ON 60 (sodium ions)
Please help
I want to use polarizable water with a membrane protein (POPC+Protein) system I built the system according to the protocols. However, i am getting a error while running grompp..
Fatal error:
Molecule type 'PW' contains no atoms
Here is my .itp file for the system (Protein_A.itp is separate and is generated with martinize.py)
; topology section
;;;;;; POLARIZABLE WATER, POPC PARAMETERS, IONS
[ moleculetype ]
; molname nrexcl
PW 1
NA+ 1
POPC 1
[ atoms ]
;id type resnr residue atom cgnr charge
1 Q0 1 POPC NC3 1 1.0
2 Qa 1 POPC PO4 2 -1.0
3 Na 1 POPC GL1 3 0
4 Na 1 POPC GL2 4 0
5 C1 1 POPC C1A 5 0
6 C1 1 POPC C2A 6 0
7 C1 1 POPC C3A 7 0
8 C1 1 POPC C4A 8 0
9 C1 1 POPC C1B 9 0
10 C1 1 POPC C2B 10 0
11 C3 1 POPC D3B 11 0
12 C1 1 POPC C4B 12 0
13 C1 1 POPC C5B 13 0
14 POL 1 PW W 1 0
15 D 1 PW WP 1 0.46
16 D 1 PW WM 1 -0.46
17 Qd 1 ION NA+ 1 1.0
#ifndef EM
[constraints]
; i j funct length
14 15 1 0.14
14 16 1 0.14
#else[bonds]
; i j funct length force const.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
14 15 1 0.14 50000
14 16 1 0.14 50000
#endif
[angles]
; i j k funct angle fc
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 120.0 45.0
11 12 13 2 180.0 25.0
15 14 16 2 0.0 4.2
[exclusions]
14 15 16
15 16
; for minimization purposes replace constraints by stiff bonds:
My .top file is as follows:
#include "martini_combined.itp"
#include "Protein_A_mod.itp"
[ system ]
; name
Martini system from 1.pdb
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
Protein_A 1
POPC 286
PW 61655 (originally it was 20555 W molecules, now I have counted WP and WM too)
ON 60 (sodium ions)
Please help
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- siewert
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- Posts: 61
12 years 3 months ago #881
by siewert
Replied by siewert on topic grompp error
Your itp and top files are all mixed up - please look at some of the example files you can find in the Download 'Example application' section for proper top and itp files, or consult the Gromacs pages on how to use Gromacs ..
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- Rajat Desikan
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- Posts: 90
12 years 3 months ago #882
by Rajat Desikan
Replied by Rajat Desikan on topic grompp error
Yes, I got it later :)...The directives were repeated in many .itp files. I merged them, and now the simulation is fine. Thanks.
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