[AMBER] confusion in xleap for ligand and comlex

From: Ayesha Kanwal <ayesha_comsian.hotmail.com>
Date: Tue, 15 Dec 2015 12:50:07 +0500

Hi dear all,
i am using amber14 and i take protein 1IMX which is very small protein, first i prepare topology files and coordinates file for ligand , receptor and complex (prmtop + inpcrd) because I want to do MMGBSA when I'm all done and also remove water molecules from the pdb file. Now for MMPBSA calcualtion i want to add solvateBox TIP3BOX 12 in complex but when i load complex pdb file. it says :
the file contained 135 atoms not in residue templates. and also did not add ions.
it means, before loading complex pdb file i have to load ligand pdb file ? or which steps i have to follow in this situation .
i follow the tutorial B0 but it is not enough for my question i already ask this question before. please guide me in this regard.
thank you
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Received on Tue Dec 15 2015 - 00:00:03 PST
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