AMBER Archive (2004)

Subject: AMBER: PDB files

From: Beale, John (
Date: Tue Jan 20 2004 - 10:43:36 CST

I have been constructing small peptides (less than 30 residues) by using Sybyl 6.91 to build the molecules and generate the pdb files. If I try to read these pdb files into LEaP, the program throws up lots of error messages and will not produce the prmtop and inpcrd files. I have found that the only way to get the pdb files read into LEaP successfully is to manually edit the pdb files, putting the atoms in the same order in which they occur in the AMBER amino acid libraries. If I do this, LEaP takes the pdb files perfectly. I don't mind doing this, but it is quite tedious. Is anyone else using Sybyl as a front end, have you noticed the same problem, and is there a workaround? Is there a program other than Sybyl that generates more faithful pdb files?


John Beale

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