[gmx-users] methanol as a solvent

[Alok Jain]

Hello
      Nuno
Thanks for advise.i did the same.
#include "ffG43a1.itp"
#include "/home/lysine/methanol/sim/methanol_WFG.itp"
and at the tail of .top file
[ molecules ]
; Compound        #mols
Protein             1
Methanol           458 (same as .itp file)

I also made some changes in full.mdp file.
i changed the group name SOL to Methanol for both tc-grps and for
energygrps.But it gave me as like:

Fatal error: Group Methanol not found in indexfile

after that i changed it to MeOH, now it is working fine but still i am
getting 3 warnings.

 here i am attaching output of grompp:-

checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 3]:
  Overriding atomtype OMET
WARNING 2 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 4]:
  Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
WARNING 3 [file "speptide.top", line 1225]:
  System has non-zero total charge: -1.342595e-05

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#  G96ANGLES:   1108
#      PDIHS:   510
#      IDIHS:   430
#       LJ14:   948
#     CONSTR:   4698
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
There are:   458      OTHER residues
There are:    19    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Not using any simulated annealing
Making dummy/rest group for Acceleration containing 1565 elements
Making dummy/rest group for Freeze containing 1565 elements
Making dummy/rest group for VCM containing 1565 elements
Number of degrees of freedom in T-Coupling group Protein is 380.63 Number
of degrees of freedom in T-Coupling group MeOH is 2745.37
Making dummy/rest group for User1 containing 1565 elements
Making dummy/rest group for User2 containing 1565 elements
Making dummy/rest group for XTC containing 1565 elements
Making dummy/rest group for Or. Res. Fit containing 1565 elements
T-Coupling       has 2 element(s): Protein MeOH
Energy Mon.      has 2 element(s): Protein MeOH
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
There were 3 warnings

gcq#196: "Clickety Clickety Click" (System Manager From Hell)


now what are the possibilities for these warnings,
i want to sort out them also,so
can u please suggest me something again.

thanks !
                                                 Alok





> Hi Alok
>
> IIRC, now you just have to edit your topology file by hand.
> Right under the #include describing the peptide, put the .itp of methanol.
>
> Like for e.g.:
>
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> #include "meoh_wfg.itp"  ; check the .itp name
>
> and at the tail of your .top file, add one line with specifying the
number of methanol molecules added to the system.
>
> Methanol 458 ; check the name of [ moleculetype ] under .itp
> And you're done.
>
> Best regards.
> Nuno
>
>
>