On Thu, Nov 18, 2021 at 5:19 PM Alan <alanwilter.gmail.com> wrote:
> Hi there,
>
> I just want to create solvent boxes, first I tried with methanol.
>
> I tried this but didn't work:
> (tleap)
> loadamberparams frcmod.meoh
> loadamberprep meoh.in
> loadOff meohbox.off
> solvateBox MOH MOH 11
> savepdb MOH moh.pdb
> saveamberparm MOH moh.prm moh.crd
>
> Errors:
> ...
> Error: For atom (.R<MOH 243>.A<HC3 4>) could not find vdW (or other)
> parameters for type (H1)
> Warning: Parameter file was not saved.
>
yes, this looks like an inconsistency in those files. The most
straightforward way to fix it seems to be to change the HC instances in the
frcmod.meoh to H1, which is what is used in the meoh.in prep file.
> But I manage to build a box this way:
> (tleap)
> loadamberprep meoh.in
> savemol2 MOH moh.mol2 1
>
> Then edit moh.mol2 so I changed atom types to lowercase and changed CT to
> c3. Then I did:
> (tleap)
> source leaprc.gaff2
> mol = loadmol2 moh1.mol2
> solvatebox mol mol 11
> saveamberparm mol moh.prm moh.crd
> savepdb mol moh.pdb
>
I'm not sure why you are switching to GAFF types here - did you want to use
the meoh in the frcmod file, or switch over to GAFF?
>
> and this worked, I could even run a simulation with gmx after converting
> amber input files with ACPYPE.
>
> What am I missing?
>
> Many thanks in advance,
> --
> Alan Silva
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Received on Mon Nov 22 2021 - 14:00:02 PST
