[gmx-users] Fatal Error: 1 molecule of MeOH in 9 molecules of H2O

Amol D. Atre ssb4 at udct.org
Wed Oct 5 08:11:34 CEST 2005


Hello all,

Trying to solvate one molecule of Methanol in 9 molecules of Water using
genbox. The Methanol.gro and Water.gro files look like following,

Pure Methanol
  648
    1MeOH   Me1    1   1.090   1.374   0.894 -0.2255  0.0272 -0.0476
    1MeOH    O2    2   1.205   1.439   0.863  0.3805 -0.9040  0.2153
    1MeOH    H3    3   1.174   1.533   0.851  0.7376 -0.5702  1.7130

Water
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
  648
    1SOL     OW    1    .230    .628    .113
    1SOL    HW1    2    .137    .626    .150
    1SOL    HW2    3    .231    .589    .021
    2SOL     OW    4    .225    .275   -.866
    2SOL    HW1    5    .260    .258   -.774
    2SOL    HW2    6    .137    .230   -.878
    3SOL     OW    7    .019    .368    .647
    3SOL    HW1    8   -.063    .411    .686
    3SOL    HW2    9   -.009    .295    .584
    4SOL     OW   10    .569   -.587   -.697
    4SOL    HW1   11    .476   -.594   -.734
    4SOL    HW2   12    .580   -.498   -.653
    5SOL     OW   13   -.307   -.351    .703
    5SOL    HW1   14   -.364   -.367    .784
    5SOL    HW2   15   -.366   -.341    .623
    6SOL     OW   16   -.119    .618    .856
    6SOL    HW1   17   -.086    .712    .856
    6SOL    HW2   18   -.068    .564    .922
    7SOL     OW   19   -.727    .703    .717
    7SOL    HW1   20   -.670    .781    .692
    7SOL    HW2   21   -.787    .729    .793
    8SOL     OW   22   -.107    .607    .231
    8SOL    HW1   23   -.119    .594    .132
    8SOL    HW2   24   -.137    .526    .280
    9SOL     OW   25    .768   -.718   -.839
    9SOL    HW1   26    .690   -.701   -.779
    9SOL    HW2   27    .802   -.631   -.875

Command line: genbox -cp Methanol.gro -cs Water.gro -o conf.gro -p topol.top

Fatal error: Invalid line in Methanol.gro for atom 4:

Can anybody please help?

Thanks in advance.

Regards,
Amol D. Atre.
Lab No.A002,
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
Matunga(E), Mumbai-400019.




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