Well, there's no real problem, per se. Everything that you've given pdb2gmx is
in the topology; the issue is that you haven't specified any parameters for
those dihedrals:
CH CB CG1 CG2
CH CB CG5 CG4
2 3 4 5 1
2 3 8 7 1
Makes sense that they'd be missing. If you're dealing with polystyrene, maybe
consider basing the dihedrals off of those contained in the PHE sidechain in the
Gromos force field you appear to be using.
-Justin
Andrea Muntean wrote:
Here are the .rtp entries:
[PS1]
[atoms]
CH3 CH3 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
[bonds]
CH3 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH +CH2 gb_26
[angles]
;109,5 angle
CH3 CH +CH2 ga_12
CH3 CH CB ga_12
CB CH +CH2 ga_12
;120 angle
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB +CH2 CH3 gi_1
CH +CH2 CH3 CB gi_1
CH CH3 CB +CH2 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
CH3 CH +CH2 +CH gd_16
CB CH +CH2 +CH gd_16
;around CH-CB - 2-fold (n=2)
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
+CH2 CH CB CG5 gd_1
+CH2 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
[PS]
[atoms]
CH2 CH2 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
[bonds]
-CH CH2 gb_26
CH2 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH +CH2 gb_26
[angles]
;109,5 angle
-CH CH2 CH ga_12
CH2 CH +CH2 ga_12
CH2 CH CB ga_12
CB CH +CH2 ga_12
;120 angle
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB +CH2 CH2 gi_1
CH +CH2 CH2 CB gi_1
CH CH2 CB +CH2 gi_1
[dihedrals]
;in the chain - 3-fold
CH2 CH +CH2 +CH gd_16
CB CH +CH2 +CH gd_16
-CH CH2 CH CB gd_16
-CH CH2 CH +CH2 gd_16
;around CH-CB - 2-fold
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
+CH2 CH CB CG5 gd_1
+CH2 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
[ PSN ]
[atoms]
CH2 CH2 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
CH3 CH3 0 0
[bonds]
-CH CH2 gb_26
CH2 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH CH3 gb_26
[angles]
-CH CH2 CH ga_12
CH2 CH CH3 ga_12
CH2 CH CB ga_12
CB CH CH3 ga_12
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB CH3 CH2 gi_1
CH CH3 CH2 CB gi_1
CH CH2 CB CH3 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
-CH CH2 CH CB gd_16
-CH CH2 CH CH3 gd_16
;around CH-CB - 2-fold (n=2)
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB CH3 CH2 gi_1
CH CH3 CH2 CB gi_1
CH CH2 CB CH3 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
-CH CH2 CH CB gd_16
-CH CH2 CH CH3 gd_16
;around CH-CB - 2-fold (n=2)
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
And the .top file for the trimer, only the [atoms] and [dihedrals]
(only the proper dihedrals) part:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CH3 1 PS1 CH3 1 0 15.035 ; qtot 0
2 CH1 1 PS1 CH 1 0 13.019 ; qtot 0
3 C 1 PS1 CB 1 0 12.011 ; qtot 0
4 CR1 1 PS1 CG1 1 0 13.019 ; qtot 0
5 CR1 1 PS1 CG2 1 0 13.019 ; qtot 0
6 CR1 1 PS1 CG3 1 0 13.019 ; qtot 0
7 CR1 1 PS1 CG4 1 0 13.019 ; qtot 0
8 CR1 1 PS1 CG5 1 0 13.019 ; qtot 0
9 CH2 2 PS CH2 2 0 14.027 ; qtot 0
10 CH1 2 PS CH 2 0 13.019 ; qtot 0
11 C 2 PS CB 2 0 12.011 ; qtot 0
12 CR1 2 PS CG1 2 0 13.019 ; qtot 0
13 CR1 2 PS CG2 2 0 13.019 ; qtot 0
14 CR1 2 PS CG3 2 0 13.019 ; qtot 0
15 CR1 2 PS CG4 2 0 13.019 ; qtot 0
16 CR1 2 PS CG5 2 0 13.019 ; qtot 0
17 CH2 3 PSN CH2 3 0 14.027 ; qtot 0
18 CH1 3 PSN CH 3 0 13.019 ; qtot 0
19 C 3 PSN CB 3 0 12.011 ; qtot 0
20 CR1 3 PSN CG1 3 0 13.019 ; qtot 0
21 CR1 3 PSN CG2 3 0 13.019 ; qtot 0
22 CR1 3 PSN CG3 3 0 13.019 ; qtot 0
23 CR1 3 PSN CG4 3 0 13.019 ; qtot 0
24 CR1 3 PSN CG5 3 0 13.019 ; qtot 0
25 CH3 3 PSN CH3 3 0 15.035 ; qtot 0
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 4 1 gd_1
1 2 3 8 1 gd_1
9 2 3 4 1 gd_1
9 2 3 8 1 gd_1
1 2 9 10 1 gd_16
3 2 9 10 1 gd_16
2 3 4 5 1
2 3 8 7 1
2 9 10 11 1 gd_16
9 10 11 12 1 gd_1
9 10 11 16 1 gd_1
17 10 11 12 1 gd_1
17 10 11 16 1 gd_1
9 10 17 18 1 gd_16
11 10 17 18 1 gd_16
10 11 12 13 1
10 11 16 15 1
10 17 18 19 1 gd_16
10 17 18 25 1 gd_16
17 18 19 20 1 gd_1
17 18 19 24 1 gd_1
25 18 19 20 1 gd_1
25 18 19 24 1 gd_1
18 19 20 21 1
18 19 24 23 1
Cheers,
Andrea
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
