[gmx-users] grompp problem

[Mark Abraham]

> Indeed.  If I just replace the CB and CR61 by C in the rtp file
> and add the bondtypes using the G53a6bon.itp then PTR is defined as
> follows

Presumably you've checked some useful source that this carbon atom type is
reasonable to use for a tyrosine ring.

> WARNING 1 [file "sh2_pep.top", line 2378]:
>   No default G96Bond types, using zeroes
> WARNING 2 [file "sh2_pep.top", line 2379]:
>   No default G96Bond types, using zeroes
> WARNING 3 [file "sh2_pep.top", line 2380]:
>   No default G96Bond types, using zeroes
> WARNING 4 [file "sh2_pep.top", line 2381]:
>   No default G96Bond types, using zeroes
> WARNING 5 [file "sh2_pep.top", line 2382]:
>   No default G96Bond types, using zeroes
> WARNING 6 [file "sh2_pep.top", line 2383]:
>   No default G96Bond types, using zeroes
> WARNING 7 [file "sh2_pep.top", line 2384]:
>   No default G96Bond types, using zeroes
> WARNING 8 [file "sh2_pep.top", line 2385]:
>   No default G96Bond types, using zeroes
> WARNING 9 [file "sh2_pep.top", line 2386]:
>   No default G96Bond types, using zeroes
> WARNING 10 [file "sh2_pep.top", line 2387]:
>   No default G96Bond types, using zeroes

So what's on these lines of your top file?

Mark