AMBER Archive (2009)

Subject: Re: [AMBER] antechamber : missed atoms

From: Khaled Barakat (kbarakat_at_phys.ualberta.ca)
Date: Mon Jan 26 2009 - 13:20:52 CST

Sorry I forgot to attache files !

> Hello,
>
> I am trying to use Antechamber from Ambertools 1.2 to get parameters for a set of ligands. The
> input pdb files for antechamber seem to be OK . Attached is an example of these ligands along
with
> the NEWPDB.PDB generated by Antechamber. As you can see there are some missing atoms in the
> NEWPDB.PDB file.
>
> I am using the command:
> antechamber -i ref.pdb -fi pdb -o ref.prepin -fo prepi -rn UNK -s 2 -at gaff
>
> and of course when I run the command
> parmchk -i ref.prepin -f prepi -o ref.frcmod
>
> I get Bus error.
>
> I am wondering if some one can help me to solve this problem and preserve these atoms?
>
> with my best regards
>
> khaled
>
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