AMBER Archive (2006)

Subject: Re: AMBER: Ring of dna

From: f m (floramactavish_at_hotmail.com)
Date: Mon Jul 17 2006 - 08:48:33 CDT

The problem is that at the stage where I type in the saveamberparm command,
I still get this error message

FATAL: Atom .R<THY 188>.A<H73 32> does not have a type

for all the atoms. Any suggestions would be appreciated. Thanks for all
the help so far.

Flora

>From: "f m" <floramactavish_at_hotmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Ring of dna
>Date: Mon, 17 Jul 2006 11:32:01 +0000
>
>I have deleated the addPdbResMap section of the leaprc.ff99 file. I think
>that would stop it from converting the final residues to terminal residues.
> I meant that my original pdb file had o3T atoms in the terminal residues.
> I have just tried changing these to O3* but that made no difference. The
>saveamberparm command won't work.
>
>
>
>>From: Bill Ross <ross_at_cgl.ucsf.edu>
>>Reply-To: amber_at_scripps.edu
>>To: amber_at_scripps.edu
>>Subject: Re: AMBER: Ring of dna
>>Date: Sat, 15 Jul 2006 10:55:07 -0700 (PDT)
>>
>> > The O3T atoms only occur on the final residues of the DNA.
>>
>>That's because your residues were converted to terminal ones
>>when you loaded the pdb, which you need to avoid by either
>>disabling the residue name mapping or using loadpdbusingseq
>>or whatever the cmd is.
>>
>>Bill
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>
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