On Thu, Jan 31, 2013 at 4:16 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Hi Brian,
>
> This is the sequence of commands I used in tleap:
>
> source leaprc.ff99SBildn
> loadAmberParams frcmod.ff99SBnmr
> WAT = T4E
> set WAT.1 name "T4E"
> loadAmberParams frcmod.tip4pew
> loadamberparams frcmod.ionsjc_tip4pew
> loadoff tip4pewbox.off
> set default FlexibleWater on
> mol = loadpdb protein.pqr
> addIons2 mol Na+ 90 Cl- 101
> solvateOct mol TIP4PEWBOX 15.1
> setBox mol vdw
>
This is your problem. solvateOct generated truncated octahedron
information in your topology and coordinate files.
setBox then gleefully overwrote that information with an orthorhombic box
surrounding your system.
Remove the setBox command and it should be fine. setBox is ONLY useful if
you have a PDB that already has a solvent box (from packmol, for instance)
and you need to add a box around that. the solvate commands in leap
automatically add the box information.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 31 2013 - 13:30:05 PST
