[AMBER] How to create a MOH box (only methanol molecules)

From: Alan <alanwilter.gmail.com>
Date: Thu, 18 Nov 2021 22:17:43 +0000

Hi there,

I just want to create solvent boxes, first I tried with methanol.

I tried this but didn't work:
loadamberparams frcmod.meoh
loadamberprep meoh.in
loadOff meohbox.off
solvateBox MOH MOH 11
savepdb MOH moh.pdb
saveamberparm MOH moh.prm moh.crd

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.

But I manage to build a box this way:
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:
source leaprc.gaff2
mol = loadmol2 moh1.mol2
solvatebox mol mol 11
saveamberparm mol moh.prm moh.crd
savepdb mol moh.pdb

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 Thu Nov 18 2021 - 14:30:03 PST
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