Odd that residues are put after waters, waters usually go last for speed
reasons.
...
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT SOD SOD SOD SOD SOD SOD SOD SOD SOD
SOD SOD
SOD SOD SOD SOD SOD
The atom types for the WATs in the prmtop are OT and HT, instead of the
normal last I remember OW and HW, so maybe you didn't load the right
water params? Send the whole leap script for clarity.
Bill
On 9/7/17 4:07 PM, David Sáez wrote:
> Hello, I am working on a system involving a protein and a small ligand
> defined in the Charmm Force field.
>
> With PSFGEN (psfscript.psf) I generated psf and pdb files of my system.
> Next, with VMD > Solvate I added water molecules and generated new psf
> files.
>
> After that I used Parmed (in Amber16) to generate prmtop and inpcrd files.
>
> But, when I run a minimization with these inpcrd and prmtop, I get the
> following error:
>
> "Error: A residue defined as a "fast 3-point water"
> is not defined by a triangle of three bonds.
> Residue 892 contains 2 bonds."
>
>
> I attach the prmtop:
> https://www.dropbox.com/s/jjmp427gyl0kfwh/emc_neutral.prmtop?dl=0
>
> Thanks in advance.
>
> David.
>
>
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Received on Thu Sep 07 2017 - 16:30:03 PDT
