Re: AMBER: problem with file format

From: David A. Case <>
Date: Wed, 24 Sep 2003 12:28:22 -0700

On Wed, Sep 24, 2003, Shafinaz wrote:
> I encountered a problem in leap. When I convert a mol2 file to pdb format in
> sybyl it lost its double bonds. However I used mol2 format for generating
> gaff atom types and then frcmod file from parmchk.

PDB files don't generally have bond type information; this doesn't sound
like a real problem.

> Then I read prep and frcmod file in leap and then when tried to read
> molecule .pdb file leap was crashed and gave me a message that bondatom
> problem see atom.c file.

This report needs more detail: can you tell us exactly what leap commands
you used? Also, you indicate that the problem arose when you loaded the
pdb file, yet you did not include any pdb file in your mail. Also, please
send the *exact* error message.

Also, please attach the files you send: the ones in your earlier mail had
extra line feeds put in them by your mailer, which makes it quite hard to
try out. I did fix up the prep file you sent, and LEaP seemed to read it in
OK. I was not able to really decipher the mol2 file you sent, but it's not
really clear that that is relevant to your problem.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Sep 24 2003 - 20:53:01 PDT
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