Thanks Carlos!
At first your tip didn't work but it made me understand the problem. First,
yes, there's this H1 x HC inconsistency.
But to get the script to work I had to add *source leaprc.protein.ff14SB*!
(verbosity 1 gave me the hint together your question why I used GAFF)
So, no this tleap.in works:
verbosity 1
source leaprc.protein.ff14SB
loadamberparams frcmod.meoh
loadamberprep meoh.in
loadOff meohbox.off
solvateBox MOH MOH 11
savepdb MOH moh.pdb
saveamberparm MOH moh.prm moh.crd
quit
But I will have different results if changing HC to H1 in frcmod.meoh.
HC mass is 1.00800 while H1 is 1.0 and so vdw diffs as well.
Bottomline, I believe frcmod.meoh needs to be updated. I'm wondering about
those who had done simulation with methanol solvent... likely this atomtype
diff wouldn't have much difference anyway.
Best,
Alan
On Mon, 22 Nov 2021 at 21:40, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
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Received on Thu Nov 25 2021 - 03:00:02 PST
