On 3/1/13 3:49 PM, Villarealed wrote:
Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error
ERROR 1 [file topol.top, line 566]:
No default G96Angle types
ERROR 2 [file topol.top, line 801]:
No default Proper Dih. types
The second error was resolved by modified the archive "residuetypes.dat".
I only add this line "SEP Protein"
To be honest I don't know how to resolve the ERROR 1.
If someone could help me I will appreciate.
Eduardo
grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr
ERROR 1 [file topol.top, line 566]:
No default G96Angle types
topol.top
[ angles ]
; ai aj ak funct c0 c1 c2
c3
1 2 3 2
newbox_solc.gro
1ACE CA 1 2.759 1.040 1.830
1ACE C 2 2.881 1.130 1.839
1ACE O 3 2.988 1.083 1.878
2SER N 4 2.872 1.258 1.805
aminoacids.rtp
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.380 1
O O -0.380 1
[ bonds ]
C CA gb_26
C O gb_4
C +N gb_9
[ angles ]
CA C +N ga_18
O C +N ga_32
[ impropers ]
C CA +N O gi_1
It looks like you are using an old version of Gromacs. This was a bug that was
fixed some time ago. There is a missing angle here:
CA C O ga_30
ERROR 2 [file topol.top, line 801]:
No default Proper Dih. types
topol.top
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
72 71 73 74 1
H N CA CB
There should not be a dihedral assigned here. It is not specified in the .rtp,
nor do the Gromos force fields assign dihedrals for H-N-X-X. The -N-CA- torsion
is defined by heavy atoms only. Are you sure the numbering is correct? The
numbers listed in topol.top correspond to the [moleculetype] numbering, which is
not necessarily the same numbering in the coordinate file, if (for example) the
residue/atom numbering does not start at 1 in the coordinate file.
-Justin
newbox_sol.gro
10SEP N 71 2.348 2.562 2.883
10SEP H 72 2.446 2.556 2.863
10SEP CA 73 2.260 2.594 2.768
10SEP CB 74 2.186 2.467 2.720
10SEP OG 75 2.110 2.424 2.827
10SEP P 76 2.001 2.314 2.797
10SEP O1P 77 2.066 2.200 2.732
10SEP O2P 78 1.949 2.275 2.928
10SEP O3P 79 1.895 2.372 2.710
10SEP C 80 2.164 2.714 2.789
10SEP O 81 2.051 2.714 2.741
aminoacids.rtp
[ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH2 0.00000 2
OG OA -0.36000 2
P P 0.94000 2
O1P OP -0.86000 2
O2P OP -0.86000 2
O3P OP -0.86000 2
C C 0.380 3
O O -0.380 3
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB OG gb_17
OG P gb_27
P O1P gb_23
P O2P gb_23
P O3P gb_23
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB OG ga_12
CB OG P ga_25
OG P O1P ga_13
OG P O2P ga_13
OG P O3P ga_13
O1P P O2P ga_28
O1P P O3P ga_28
O2P P O3P ga_28
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB OG gd_17
CA CB OG P gd_14
CB OG P O1P gd_11
-----
Eduardo Villarreal RamÃrez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
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--
========================================
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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