On Mon, Apr 07, 2014, Lara rajam wrote:
> I was able to proceed with all the commands, but the topology file is not
> generated
>
> I have the following error
....your snippet didn't show any errors, just warnings. But there must have
been errors, so look carefully in the leap.log file.
>
> O -SO 0.00 0.000 ATTN, need revision
> SO-OS 0.00 0.000 ATTN, need revision
This looks odd, since the atom types are in upper case, but gaff atom types
are always lower case. There is almost certainly something wrong with the
structure, or with the ways in which antechamber is identifying atoms types:
did you ask for "-at amber"? (don't do that, unless you know your molecule
has just the sorts of functional groups found in proteins or nucleic acids.)
...good luck...dac
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Received on Mon Apr 07 2014 - 12:30:03 PDT
