Hello all,
I have the same problem, but I think the dihedral is properly defined.
I am running a polymer with the G53A6 force field. First I use pdb2gmx to
generate a conf and a top file. When I run grompp, I have the error(s):
ERROR 1 [file topol.top, line 1507]:
No default Proper Dih. types
Then I go to the topol.top file, line 1507, which contains, inside the [
dihedrals ] directive:
1 2 10 11 1
It is clear that it does not have a torsion type defined for this atoms. I
look at the beginning of the same top file, to know of what type are atoms
1, 2, 10, and 11, and in what residue they are:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 CH3 1 MEA CB 1 0 15.035 ; qtot
0
2 CH1 2 NIP CA1 2 0 13.019 ; qtot
0
3 C 2 NIP C 3 0.45 12.011 ; qtot
0.45
4 O 2 NIP O 3 -0.45 15.9994 ; qtot
0
5 N 2 NIP N 4 -0.31 14.0067 ; qtot
-0.31
6 H 2 NIP H 4 0.31 1.008 ; qtot
0
7 CH1 2 NIP CA2 5 0 13.019 ; qtot
0
8 CH3 2 NIP CB1 5 0 15.035 ; qtot
0
9 CH3 2 NIP CB2 5 0 15.035 ; qtot
0
10 CH2 3 MEM CB 6 0 14.027 ; qtot
0
11 CH1 4 NIP CA1 7 0 13.019 ; qtot
0
...etc
Now I look to my aminoacids.rtp file. There I have the residues defined:
[ MEA ]
[ atoms ]
CB CH3 0.000 1
[ bonds ]
[ MEM ]
[ atoms ]
CB CH2 0.000 1
[ bonds ]
CB -CA1 gb_27
[ angles ]
CB -CA1 -CB ga_15
[ MEE ]
[ atoms ]
CB CH3 0.000 1
[ bonds ]
CB -CA1 gb_27
[ angles ]
-CB -CA1 CB ga_15
[ NIP ]
[ atoms ]
CA1 CH1 0.000 1
C C 0.450 2
O O -0.450 2
N N -0.310 3
H H 0.310 3
CA2 CH1 0.000 4
CB1 CH3 0.000 4
CB2 CH3 0.000 4
[ bonds ]
CA1 C gb_27
C O gb_5
C N gb_11
N H gb_2
N CA2 gb_21
CA2 CB1 gb_27
CA2 CB2 gb_27
CA1 -CB gb_27
[ angles ]
-CB CA1 +CB ga_15
-CB CA1 C ga_13
C CA1 +CB ga_13
CA1 C O ga_30
CA1 C N ga_19
O C N ga_33
C N H ga_32
C N CA2 ga_31
H N CA2 ga_18
N CA2 CB1 ga_13
N CA2 CB2 ga_13
CB1 CA2 CB2 ga_15
CA1 +CB +CA1 ga_15
[ dihedrals ]
-CB CA1 +CB +CA1 gd_34
-CB CA1 C N gd_40
CA1 C N CA2 gd_14
C N CA2 CB1 gd_39
CA1 +CB +CA1 +C gd_34
[ impropers ]
CA1 -CB +CB C gi_2
C CA1 N O gi_1
N C CA2 H gi_1
CA2 N CB1 CB2 gi_2
As I understand it, the torsion grompp is complaining about is the first
torsion defined in the NIP residue. I have tried, just in case, to write
that torsion in different ways, at a different order, in the residue MEM,
changing atom names to the name they have in atomtypes.atp... but without
success.
Any idea what happens?
Kind regards
--
View this message in context:
http://gromacs.5086.n6.nabble.com/No-default-Proper-Dih-types-tp4442749p5004621.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
