Moreover, it doesn't recognize the ions in tleap, although it was kept
in the converting output file:
--------tleap log------------
For atom: .R<K+ 774>.A<K+ 1> Could not find type: K+
For atom: .R<Cl- 737>.A<Cl- 1> Could not find type: Cl-
-----------ions-----in-----------charmmgui2amber--------output-----------
ATOM 38327 K+ K+ 6439 39.190 7.670 33.910 1.00 0.00 POT
ATOM 38379 Cl- Cl- 6491 45.570 43.770 81.080 1.00 0.00 CLA
On 05/08/2012 09:44 PM, Benjamin D Madej wrote:
> Hi Albert,
>
> The script was designed for CHARMM-GUI pdb files. It sounds like the gromacs file has atoms that are named differently in POPE (or extra atoms?). Take a look to see which atoms still have the POPE label to see the differences.
>
> Those warnings are normal for loading PDBs with Lipid11 in leap.
>
> Best,
> Ben Madej
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Received on Wed May 09 2012 - 02:30:04 PDT
