[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

[Justin Lemkul]

On 7/13/14, 8:14 PM, vivek sinha wrote:
> Thanks Justin.
> But when I am trying to run the energy minimization I get the
> error message "No such moleculetype SOL"
>
> The minim.mdp file that I am using for energy minimization is:
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emtol        = 1000.0      ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps        = 50000          ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist            = 1            ; Frequency to update the neighbor list
> and long range forces
> cutoff-scheme   = Verlet
> ns_type            = grid        ; Method to determine neighbor list
> (simple, grid)
> coulombtype        = PME        ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0        ; Short-range electrostatic cut-off
> rvdw            = 1.0        ; Short-range Van der Waals cut-off
> pbc                = xyz         ; Periodic Boundary Conditions (yes/no)
>
>
> Can you please suggest how to solve this error.
>

The only modification to your topology that you need to make is to adjust the 
number of SOL molecules in the [molecules] directive.  Doing that won't give 
rise to this error.  The error itself is telling you that the SOL moleculetype 
has not been declared, i.e. you have not #included a water topology appropriately.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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