AMBER Archive (2009)

Subject: RE: [AMBER] loadpdb atom type

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue May 19 2009 - 13:15:02 CDT

It says:

 Leap added 451 missing atoms according to residue templates:
       451 H / lone pairs
  The file contained 444 atoms not in residue templates

I don't understand this thing about columns. Do I need to shift a column or something? Is it syntax?
Thanks
________________________________________

From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling_at_gmail.com]
Sent: Tuesday, May 19, 2009 1:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] loadpdb atom type

it's probably not the names themselves, but the columns the names use in the
file. does leap say anything about having extra atoms?

On Tue, May 19, 2009 at 12:20 PM, Mark M Huntress <markmh_at_bgsu.edu> wrote:

> Hi, I have a pdb that was saved on VMD, and AMBER doesn't want to load it
> right.
>
> It creates about 400 new hydrogens, because it apparently cannot recognize
> the hydrogens that are already there.
>
> For example, these are some of the H's it adds when I do "mol = loadpdb
> file.pdb" :
> Created a new atom named: 2HB within residue: .R<ARG 136>
> Created a new atom named: 3HB within residue: .R<ARG 136>
> Created a new atom named: 2HG within residue: .R<ARG 136>
> Created a new atom named: 3HG within residue: .R<ARG 136>
> Created a new atom named: 2HD within residue: .R<ARG 136>
> Created a new atom named: 3HD within residue: .R<ARG 136>
>
> but these atoms are already in the pdb file:
>
> ATOM 2146 N ARG A 136 -15.329 -2.598 -9.210 1.00 0.00
> ATOM 2147 H ARG A 136 -15.332 -3.533 -9.614 1.00 0.00
> ATOM 2148 CA ARG A 136 -15.497 -1.426 -10.034 1.00 0.00
> ATOM 2149 HA ARG A 136 -14.896 -0.566 -9.736 1.00 0.00
> ATOM 2150 CB ARG A 136 -15.344 -1.704 -11.501 1.00 0.00
> ATOM 2151 2HB ARG A 136 -15.675 -2.780 -11.830 1.00 0.00
> ATOM 2152 3HB ARG A 136 -15.854 -0.894 -12.075 1.00 0.00
> ATOM 2153 CG ARG A 136 -13.870 -1.699 -11.959 1.00 0.00
> ATOM 2154 2HG ARG A 136 -13.437 -0.753 -11.777 1.00 0.00
> ATOM 2155 3HG ARG A 136 -13.283 -2.423 -11.422 1.00 0.00
> ATOM 2156 CD ARG A 136 -13.865 -2.007 -13.406 1.00 0.00
> ATOM 2157 2HD ARG A 136 -14.316 -2.963 -13.526 1.00 0.00
> ATOM 2158 3HD ARG A 136 -14.529 -1.226 -13.934 1.00 0.00
> ATOM 2159 NE ARG A 136 -12.541 -1.883 -14.120 1.00 0.00
> ATOM 2160 HE ARG A 136 -12.134 -0.944 -14.162 1.00 0.00
> ATOM 2161 CZ ARG A 136 -11.668 -2.878 -14.399 1.00 0.00
> ATOM 2162 NH1 ARG A 136 -11.836 -4.163 -14.169 1.00 0.00
> ATOM 2163 1HH1 ARG A 136 -12.614 -4.424 -13.626 1.00 0.00
> ATOM 2164 2HH1 ARG A 136 -11.124 -4.965 -14.312 1.00 0.00
> ATOM 2165 NH2 ARG A 136 -10.626 -2.634 -15.083 1.00 0.00
> ATOM 2166 1HH2 ARG A 136 -10.436 -1.665 -15.341 1.00 0.00
> ATOM 2167 2HH2 ARG A 136 -10.050 -3.400 -15.471 1.00 0.00
> ATOM 2168 C ARG A 136 -16.923 -0.961 -9.830 1.00 0.00
> ATOM 2169 O ARG A 136 -17.896 -1.685 -9.808 1.00 0.00
>
>
> Is this maybe a problem with atom order? Is there something simple that I
> am missing?
>
> Thanks,
> Mark
>
>
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