From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Dec 11 2015 - 08:45:00 CST
When did you add in the coordpdb line? Was it above or below this
section? If atom positions aren't initialized, they will be put at the
origin by default, which is normally not what people want. My guess is
that you put it above the section, so that psfgen came across atoms it
didn't recognize and ignored them, only to have you patch them in
afterward with the coordinates placed at the origin.
-Josh Vermaas
On 12/11/2015 05:07 AM, Francesco Pietra wrote:
> Hello:
>
> With CHARMM36, VMD in text mode, the .gen file including:
>
> patch GLUP PRA:235
> patch ASPP PRA:516
>
> regenerate angles dihedrals
>
> (the protein pdb included all H-atoms), the log file reports that it
> was unable to read HE2 and HD2 for the above residues. The result was
> that these atoms were put outside the protein.
>
> On removing HE2 and HD2 from the pdb, no more such warnings, however,
> again, both atoms placed outside the protein. Apparently the patch was
> accepted.
> ..............................
>
> Moreover, despite the error reported in the log file;
>
> psfgen) Toplogy and parameter information for water and ions.
> psfgen)
> psfgen) ERROR! FAILED TO RECOGNIZE SET
> psfgen) ERROR! FAILED TO RECOGNIZE SET
> psfgen) ERROR! FAILED TO RECOGNIZE IF
> psfgen) ERROR! FAILED TO RECOGNIZE READ
> psfgen) Topology for water and ions
> psfgen)
> psfgen) ERROR! FAILED TO RECOGNIZE 31
> psfgen) skipping statements at end of file due to end or return statement
>
> a ligand CLA of the protein was set correctly. is there any possible
> modification of the str file, or should I extract from it the relevant
> portions in order to skip what VMD is unable to read from CHARMM36?
> ......................................
>
> Grateful for advice
>
> francesco pietra
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