AMBER Archive (2003)

Subject: Re: probelms with antechamber

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 20 2003 - 19:19:24 CST

On Thu, Feb 20, 2003, Yongmei Wang wrote:
>
> Hi, I tried to use antechamer for a HIV-PR inhibitor called MK1.
> I successefully run the command:
> antechamber -i MK1H.pdb -fi pdb -o mk1.prepi -fo prepi
>
> Then I ran the pamrchk, the output of frcmod does not contain any warning
> lines.
> Then I used to leap to load in the mk1.prepi, and then try to load the
> molecule MK1H.pdb, but the program died the minute I loaded the pdb file.

Since the problem occurred on loading the pdb file, it would have been best to
send the pdb file in your mail. Otherwise, we have not way to try to
reproduce the error. However, on looking at the prep file you sent, it looks
like you have many atoms with the same name (e.g. "H"). All atom names within
a residue must be unique. I don't know if this is what is causing the problem
or not.

> THe error message says:
>
> FATAL: In file [atom.c], line 443
> FATAL: Message: bondAtomProblem found

But what does it say above these lines?? There should be something
like "ATOMS NOT BONDED", plus some information that would be helpful.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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