I see that VOTCA is running the following command:
gmx_196 grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c
conf.gro
And I am getting the following error:
Molecule type PNM contains no atoms
This is my topol.top file:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 0.0 0.0
[ atomtypes ]
; type mass charge ptype sigma epsilon
TB 29.04 0.000 A 0.0000 1.0000
TA 43.00 0.000 A 0.0000 1.0000
TI 43.00 0.000 A 0.0000 1.0000
TW 18.01 0.000 A 0.0000 1.0000
[ moleculetypes ]
; Name nrexcel
PNM 3
WT 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 TB 1 PNM BB 1 0 29.04
2 TA 1 PNM BA 1 0 43.00
3 TI 1 PNM BI 1 0 43.00
4 TW 1 WT BW 1 0 18.01
[ bonds ]
;ai aj funct c0 c1 c2 c3
1 2 8 1 1.0
2 3 8 1 1.0
[ angles ]
;ai aj ak funct c0 c1 c2
1 2 3 8 1 1.0
[ molecules ]
;
PNM 1
WT 4046
I don’t understand what is causing this error. I have written similar types
of topol.top files, and it seems to be working just fine.
For completeness sake, this is my conf.gro file:
what a nice title
4049
1PNM BB 1 2.229 1.514 4.238
1PNM BA 2 2.272 1.286 4.235
1PNM BI 3 2.194 1.048 4.125
2WT BW 4 2.276 1.580 1.676
3WT BW 5 0.119 0.703 0.277
4WT BW 6 1.682 0.128 4.229
5WT BW 7 4.889 2.252 2.343
.
.
.
4045WT BW 4047 1.332 2.041 1.148
4046WT BW 4048 0.125 1.348 4.089
4047WT BW 4049 0.839 1.673 3.898
4.98674 4.98674 4.98674 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000
I would appreciate any advice you have for me!
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