AMBER Archive (2007)

Subject: Re: AMBER: xLeap "Could not find type" error

From: Wei Zhang (zweig_at_scripps.edu)
Date: Wed Aug 22 2007 - 10:18:11 CDT

Hi,

looks like you have hydrogens in your pdb file.

try to remove all the hydrogens in your file and load again.

Sincerely,

Wei

WANG,YING wrote:

> HI, DEAR AMBER MEMBERS,
> I also have the "could not find type" problem when I run the xleap.
> The message as below:
>
>> xx=loadpdb "xx.pdb"
>
> loading pdb file: ./xx.pdb
> created a new atom named: H within residue: .R<NPHE 1>
> ...
> ...
> Leap added 19 missing atoms according to residue templates:
> 19H/long pairs
> The file contained 17 atoms not in residue templates
>
>
>> saveamberparm xx xx.prmtop xx.inpcrd
>
> Checking unit.
> FATAL: ATOM .R<NPHE 1>.A<H 23>does not have a type
> ...
> ...
> Failed to generate parameters
>
> This pdb file was downloaded from PDB bank. I check it but cannot
> figure out what's happen............. Could you help me? Thanks very
> much!!
>
>
>
>
>
>
>
>
> --
> WANG,YING
> Mechanical and Aerospace Engineering
> University of Florida
>
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