AMBER Archive (2009)

Subject: [AMBER] ambpdb is changing atom names, a feature or bug?

From: Markus Kaukonen (markus.kaukonen_at_iki.fi)
Date: Fri Jan 09 2009 - 06:55:41 CST

Dear Amber,

I issue (in Amber 10)
ambpdb -pqr -p prmtop < prmcrd > test.pdb

but the atom names are not the same in 'prmtop' file and in 'test.pdb'
file (as I would like).
:atom 9 changed from H3 to 2H, atom 20 changed from H1 to 1H, last
atom 22 changed from H2 to 2H.

in prmtop file one has
%FLAG ATOM_NAME
%FORMAT(20a4)
C6 H7 H8 H9 C5 H5 H6 C4 H3 H4 N C H N1 C3 H10 H11 H12 C1 H1
C2 H2

and in the resulting pdb file (test.pdb)
REMARK
ATOM 1 C6 PM2 1 -3.890 -0.323 0.223 -0.3159 1.700
ATOM 2 H7 PM2 1 -4.023 -1.313 -0.202 0.0956 1.300
ATOM 3 H8 PM2 1 -4.505 -0.260 1.112 0.0956 1.300
ATOM 4 H9 PM2 1 -4.264 0.404 -0.490 0.0956 1.300
ATOM 5 C5 PM2 1 -2.426 -0.058 0.574 0.2222 1.700
ATOM 6 H5 PM2 1 -2.327 0.925 1.024 -0.0057 1.500
ATOM 7 H6 PM2 1 -2.081 -0.779 1.309 -0.0057 1.500
ATOM 8 C4 PM2 1 -1.537 -0.142 -0.665 -0.1718 1.700
ATOM 9 2H PM2 1 -1.831 0.578 -1.415 0.1197 1.300
ATOM 10 H4 PM2 1 -1.586 -1.124 -1.116 0.1197 1.300
ATOM 11 N PM2 1 -0.118 0.117 -0.353 0.0986 1.550
ATOM 12 C PM2 1 0.830 -0.788 -0.246 -0.0252 1.700
ATOM 13 H PM2 1 0.697 -1.838 -0.396 0.2377 1.500
ATOM 14 N1 PM2 1 1.968 -0.208 0.071 0.1519 1.550
ATOM 15 C3 PM2 1 3.258 -0.874 0.269 -0.3096 1.700
ATOM 16 H10 PM2 1 3.615 -0.670 1.267 0.1638 1.500
ATOM 17 H11 PM2 1 3.124 -1.938 0.145 0.1638 1.500
ATOM 18 H12 PM2 1 3.964 -0.511 -0.462 0.1638 1.500
ATOM 19 C1 PM2 1 1.741 1.147 0.173 -0.1695 1.700
ATOM 20 1H PM2 1 2.520 1.836 0.418 0.2483 1.500
ATOM 21 C2 PM2 1 0.440 1.349 -0.090 -0.2547 1.700
ATOM 22 2H PM2 1 -0.134 2.249 -0.118 0.2818 1.500
TER
END

The full files prmtop and prmcrd are attached.

Terveisin, Markus 

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  • application/octet-stream attachment: prmtop
  • application/octet-stream attachment: prmcrd

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