On Tue, May 04, 2010, ashutosh shandilya wrote:
> To generate the topology and crd file I used these commands for
> protein,complex and drug
> tleap
> source leaprc.gaff
> loadamberprep drug.prepin
> loadamberparams drug.frcmod
> var=loadpdb complex.pdb
> saveamberparm var complex.top complex.crd
> addions var Na+ 0
> solvatebox var TIP3PBOX 8.0
> solvateoct var TIP3PBOX 8.0
Ouch...You are supposed to use either "solvatebox" OR "solvateoct", not
both of them. The program is probably quite confused at this point. You need
to choose whether you want a rectangular box or a truncated octahedron.
...hope this helps....dac
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Received on Tue May 04 2010 - 05:00:05 PDT
