AMBER Archive (2009)

Subject: Re: [AMBER] creating new residue adds none wanted ter

• Previous message: Remya S R: "[AMBER] Charge problem"
• In reply to: Jorgen Simonsen: "Re: [AMBER] creating new residue adds none wanted ter"
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On Tue, May 05, 2009, Jorgen Simonsen wrote:
>
> 1. The residues look fine around the residue so I don't that causes the
> problem.

I suppose you should post that portion of the PDB file. What looks "fine" to
you might still be a problem.

>
> 2. I am not able to generate prmtop where I get the following error message
> FATAL: Atom .R<ILE 277>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 303>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 314>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 328>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 334>.A<CD 20> does not have a type.

I'm betting there are also lots of earlier messages ("adding new atom")
related to this. The PDB/IUPAC/Amber name for this atom is indeed "CD1", not
"CD". You will need to edit the PDB file to use the correct names.

...dac

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• Previous message: Remya S R: "[AMBER] Charge problem"
• In reply to: Jorgen Simonsen: "Re: [AMBER] creating new residue adds none wanted ter"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]