AMBER Archive (2004)

Subject: Re: AMBER:

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 31 2004 - 22:56:27 CDT

On Mon, Aug 30, 2004, jwcraft_at_uh.edu wrote:
>
> I developed the automation script after getting one successful
> dyana->leap->sander run completed. It should have worked correctly,
> however the same error occurred. FATAL: Atom .R NCYS 1.A HS 14 does not
> have a type. I have now discovered that I had correctly modified the
> nomenclature for the cysteine residue's proton on the sulfur atom. I
> had in fact used HSG as required. That solution was masked because
> protonate also changes nomenclature and over wrote my fix. Now I have
> added a sed line:
>
> sed -e 's/ HG /CYS/HSG CYS/' < leap_temp.apdb > leap_temp_pro.pdb
>
> after protonate has updated the file and before leap processes the data

I am not able to figure out your problem. "HG" is the name used in all
amber libraries (except for the very old united atom residues). Your
web site indicates that you found a line with "HSG" in it, but it doesn't say
exactly which file this was found in. Using leaprc.ff99 should give you
"HG" as the cysteine proton name.

So I think we will need more details about exactly what you are doing...I
can't see how to reproduce the problem you are seeing.

...regards...dac

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