On Sun, Nov 9, 2014 at 9:31 PM, LI An-Bang <anbangli.qq.com> wrote:
> Hi, all,
>
>
> I used pdb4amber to convert some pdb files, and I found there maybe some
> problems of pdb4amber in converting pdb files.
>
>
> The original pdb file is 1NB5, which have some insertion residues. For
> example, there is a residue numberd as "10A" in the following segment:
> (Acording to http://www.wwpdb.org/documentation/format33/sect9.html#ATOM,
> column 27 is "Code for insertion of residues". And, "Alphabet letters are
> commonly used for insertion code. The insertion code is used when two
> residues have the same numbering. The combination of residue numbering and
> insertion code defines the unique residue.")
>
>
> ATOM 83 N LYS A 10 30.107 -15.634 23.138 1.00 67.08
> N
> ATOM 84 CA LYS A 10 28.941 -15.747 24.014 1.00 56.56
> C
> ATOM 85 C LYS A 10 27.928 -16.733 23.455 1.00 61.37
> C
> ATOM 86 O LYS A 10 27.328 -17.517 24.192 1.00 62.22
> O
> ATOM 87 CB LYS A 10 28.270 -14.383 24.191 1.00 54.77
> C
> ATOM 88 CG LYS A 10 29.093 -13.376 24.965 1.00 55.52
> C
> ATOM 89 CD LYS A 10 28.238 -12.645 25.979 0.00 61.74
> C
> ATOM 90 CE LYS A 10 29.044 -12.324 27.226 0.00 65.26
> C
> ATOM 91 NZ LYS A 10 28.449 -11.179 27.972 0.00 55.65
> N
> ATOM 92 N GLY A 10A 27.739 -16.676 22.143 1.00 62.44
> N
> ATOM 93 CA GLY A 10A 26.810 -17.569 21.489 1.00 65.12
> C
> ATOM 94 C GLY A 10A 26.878 -17.423 19.979 1.00 65.60
> C
> ATOM 95 O GLY A 10A 27.953 -17.302 19.387 1.00 71.81
> O
> ATOM 96 N ASN A 11 25.713 -17.477 19.351 1.00 66.31
> N
> ATOM 97 CA ASN A 11 25.587 -17.341 17.907 1.00 55.56
> C
> ATOM 98 C ASN A 11 25.044 -15.927 17.772 1.00 48.85
> C
> ATOM 99 O ASN A 11 23.845 -15.717 17.594 1.00 65.33
> O
>
>
>
>
>
>
>
> After convertion of pdb4amber, the segment is follows, in which the "10A"
> residue is written as residue "11" and "12". It was messed up!
>
>
> ATOM 83 N LYS A 10 30.107 -15.634 23.138 1.00 67.08
> N
> ATOM 84 CA LYS A 10 28.941 -15.747 24.014 1.00 56.56
> C
> ATOM 85 C LYS A 10 27.928 -16.733 23.455 1.00 61.37
> C
> ATOM 86 O LYS A 10 27.328 -17.517 24.192 1.00 62.22
> O
> ATOM 87 CB LYS A 10 28.270 -14.383 24.191 1.00 54.77
> C
> ATOM 88 CG LYS A 10 29.093 -13.376 24.965 1.00 55.52
> C
> ATOM 89 CD LYS A 10 28.238 -12.645 25.979 0.00 61.74
> C
> ATOM 90 CE LYS A 10 29.044 -12.324 27.226 0.00 65.26
> C
> ATOM 91 NZ LYS A 10 28.449 -11.179 27.972 0.00 55.65
> N
> ATOM 92 N GLY A 11 27.739 -16.676 22.143 1.00 62.44
> N
> ATOM 93 CA GLY A 12 26.810 -17.569 21.489 1.00 65.12
> C
> ATOM 94 C GLY A 12 26.878 -17.423 19.979 1.00 65.60
> C
> ATOM 95 O GLY A 12 27.953 -17.302 19.387 1.00 71.81
> O
>
You're right, this is a problem. It was actually a known problem and was
fixed shortly before Amber 14 was released, but unfortunately the fix never
made its way into the version of the code that wound up getting released.
Romain asked me to release an update to back-port the fix to Amber 14 about
2 months ago, but I forgot. Thanks for reminding me.
I've made the fix and added the update to the website.
Please try to re-configure Amber 14 in serial and recompile it. pdb4amber
should then work (as in, 10A becomes residue 11 and the remaining residues
get incremented. As Dave said, Amber is limited to considering residues
numbered sequentially starting from 1).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 10 2014 - 05:00:02 PST
