AMBER Archive (2003)

Subject: Re: AMBER: Antechamber & Ptraj/Rdparm

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Dec 31 2003 - 05:44:00 CST

Thank you for reply. But some users said they can use ambpdb to get new pdb
file from prmtop & inpcrd files. And the new pdb file should be read back to
leap to add solvent. But I tried this ambpdb command as following:

ambpdb -p 60.prmtop < restrt > new.pdb

But I still cannot use loadpdb command to load it to the leap. Anybody can help
me? Thank you in advance.

Lan

Quoting Bill Ross <ross_at_cgl.ucsf.edu>:

> > *I cannot load the pdb file into the xleap without loading
> > the prep file after I got the charges and atom types from ANTECHAMBER?
>
> Exactly - the prep files are the templates to which the pdb
> residues are matched, so must be loaded before the pdb. If
> this is not done, new, parameterless residues are created
> for the ones that lack templates.
>
> Bill Ross
>
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