On 1/16/13 10:58 AM, escajarro wrote:
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?
Atom names and .rtp files are largely irrelevant here. You have a torsion
specified with atom types CH3-CH1-CH2-CH1. If there are no parameters in
ffbonded.itp for that interaction, grompp is going to give you that error message.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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