AMBER Archive (2009)

Subject: [AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA

From: Vikas Sharma (
Date: Mon Apr 13 2009 - 15:11:07 CDT

Dear All,
when i load my mol2 file containing the protein & ligand and try to save it i find error..
(Actually i hve incorrect ligand structure in my PDB  protein with co-crystaliized with ligand, so i tried to correct the ligand in sybyl7.1 and merge with the protein..but after saving it in PDB format when i open it again i find the same wrong structure...)
can i use that pdb co-crystallized with the wrong ligand?
can i use a partially minimized protein using proteij preparation wizard of Glide software?
please suggest a solution?????

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