Hi,
Consider this rna pdb file snippet with explicit hydrogens:
ATOM 32 P C A 2 3.336 5.775 -7.177 1.00 0.00 P
ATOM 33 O1P C A 2 2.341 5.883 -8.269 1.00 0.00 O
ATOM 34 O2P C A 2 4.239 4.603 -7.115 1.00 0.00 O
ATOM 35 N1 C A 2 -1.330 8.585 -6.056 1.00 0.00 N
ATOM 36 C2 C A 2 -2.491 9.347 -6.112 1.00 0.00 C
ATOM 37 O2 C A 2 -3.031 9.744 -5.083 1.00 0.00 O
ATOM 38 N3 C A 2 -3.022 9.638 -7.329 1.00 0.00 N
ATOM 39 C4 C A 2 -2.440 9.198 -8.451 1.00 0.00 C
ATOM 40 N4 C A 2 -3.002 9.526 -9.606 1.00 0.00 N
ATOM 41 C5 C A 2 -1.251 8.410 -8.404 1.00 0.00 C
ATOM 42 C6 C A 2 -0.732 8.129 -7.196 1.00 0.00 C
ATOM 43 C1* C A 2 -0.751 8.297 -4.722 1.00 0.00 C
ATOM 44 C2* C A 2 -1.574 7.289 -3.927 1.00 0.00 C
ATOM 45 C3* C A 2 -1.052 5.992 -4.519 1.00 0.00 C
ATOM 46 C4* C A 2 0.445 6.264 -4.589 1.00 0.00 C
ATOM 47 C5* C A 2 1.193 5.464 -5.651 1.00 0.00 C
ATOM 48 H1* C A 2 -0.638 9.221 -4.154 1.00 0.00 H
ATOM 49 H2* C A 2 -2.641 7.411 -4.112 1.00 0.00 H
ATOM 50 H3* C A 2 -1.488 5.763 -5.491 1.00 0.00 H
ATOM 51 H4* C A 2 0.894 6.081 -3.613 1.00 0.00 H
ATOM 52 H41 C A 2 -3.732 10.185 -9.376 1.00 0.00 H
ATOM 53 H42 C A 2 -2.753 9.187 -10.524 1.00 0.00 H
ATOM 54 H5 C A 2 -0.783 8.051 -9.309 1.00 0.00 H
ATOM 55 1H5* C A 2 1.174 4.409 -5.377 1.00 0.00 H
ATOM 56 2H5* C A 2 0.694 5.593 -6.612 1.00 0.00 H
ATOM 57 H6 C A 2 0.168 7.536 -7.126 1.00 0.00 H
ATOM 58 2HO* C A 2 -1.300 8.289 -2.249 1.00 0.00 H
ATOM 59 O2* C A 2 -1.272 7.371 -2.530 1.00 0.00 O
ATOM 60 O3* C A 2 -1.261 4.951 -3.552 1.00 0.00 O
ATOM 61 O4* C A 2 0.530 7.665 -4.900 1.00 0.00 O
ATOM 62 O5* C A 2 2.558 5.889 -5.770 1.00 0.00 O
To head off free advice on hydrogens, explicit hydrogens with these
coordinates are needed for scientific comparisons.
Leap processing via
source leaprc.rna.ff94
x=loadPdb noh.pdb
savePdb x noh.amber.pdb
saveAmberParm x noh.prmtop noh.inpcrd
quit
produces:
...
Created a new atom named: H2* within residue: .R<RC3 2>
total atoms in file: 31
Leap added 2 missing atoms according to residue templates:
2 H / lone pairs
The file contained 1 atoms not in residue templates
FATAL: Atom .R<RC3 2>.A<H2* 33> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Why is it that none of these atom maps fixes the naming problem
addPdbAtomMap { { "H2*" "1H2*" } }
addPdbAtomMap { { "H2*" "H2*1" } }
addPdbAtomMap { { "H2*" "1H2'" } }
addPdbAtomMap { { "H2*" "1H2" } }
addPdbAtomMap { { "H2*" "H2'" } }
but that this one does
addPdbAtomMap { { "H2*" "H2'1" } }
??
Note that leap's savepdb uses the atom name 1H2*.
Also what are the perils of always using
addPdbAtomMap { { "H2*" "H2'1" } }
when reading rna pdb's ?
thanks,
Scott
Received on Sun Mar 25 2007 - 06:07:33 PDT
