AMBER Archive (2009)

Subject: RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels

From: Tomasio, Susana (S.M.T.Tomasio_at_warwick.ac.uk)
Date: Wed May 27 2009 - 07:13:58 CDT

Hi David

Thank you for your reply.

Yes I sorted the other problems. Apparently I was doing some mistakes and now all those are problems are sorted.

Thank you,

Susana

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of David A. Case
Sent: Wed 5/27/2009 12:57 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels
 
On Wed, May 27, 2009, Tomasio, Susana wrote:
>
> I noticed that the N-cap residue Acetyl (ACE) in the amoeba force field
> is in two files (amoeba_amino.off and amoeba_aminont.off), but has
> different atom labels (2nd column): One is labelled with numbers and the
> other one is labelled with letters.

> In the amoeba_amino.off:
> "HH31" "181" 0 1 131072 1 1 0.076010
> "CH3" "180" 0 1 131072 2 6 -0.190264
> "HH32" "181" 0 1 131072 3 1 0.076011
> "HH33" "181" 0 1 131072 4 1 0.076010
> "C" "182" 0 1 131072 5 6 0.512403
> "O" "183" 0 1 131072 6 8 -0.550170
>
> And in the amoeba_aminont.off:
> "HH31" "HC" 0 1 131072 1 1 0.112300
> "CH3" "CT" 0 1 131072 2 6 -0.366200
> "HH32" "HC" 0 1 131072 3 1 0.112300
> "HH33" "HC" 0 1 131072 4 1 0.112300
> "C" "C" 0 1 131072 5 6 0.597200
> "O" "O" 0 1 131072 6 8 -0.567900
>
> When I tried to load the ACE residue it didn't work, but by changing the
> 2nd column in the amoeba_aminont.off to include the labels that are in
> the the amoeba_amino.off file, it did work.

Thanks for the note. This certainly looks like a bug. I'm cc-ing this to Wei
Zhang, who is our (only?) amoeba expert, but to me, what you did looks
correct: the other entries in amoeba_aminont.off us numbers for atom types.

Did you ever solve the other problems you were having with amoeba simulations?
I've been leaving that up to Wei as well, but we can probably recruit others
to look at this if needed. If you are having problems, are there any
differences between pmemd.amba and sander? That might help pin down the
problem.

...thanks!...dac

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