Marc Charendoff wrote:
Hey all,
I am trying to pdb2gmx a pdb file using the 43a1 force field and
despite my checking the .atp and .rtp files, I still get the following
error . . .
Back Off! I just backed up posre_A.itp to ./#posre_A.itp.2#
Processing chain 2 '+' (2 atoms, 1 residues)
This is a good clue - pdb2gmx is finding a chain called "+" even though your
structure is chain "A" - your format is incorrect.
<snip>
*BUT . . . . I thought I DID use ZN2+. *
ATOM 1912 CG2 ILE A 240 22.637 28.530 -5.925 1.00 16.18
.000
ATOM 1913 CD1 ILE A 240 22.075 30.322 -3.413 1.00 16.47
.000
ATOM 1914 ZN2+ ZN2+ A 241 11.832 23.652 11.052 1.00 20.05
.000
If you have a four-character atom name, you have to offset the start of the atom
name by -1, so the alignment should be:
CD1
ZN2+
not:
CD1
ZN2+
-Justin
ATOM 1915 ZN2+ ZN2+ A 242 11.551 25.149 14.101 1.00 23.28
.000
ATOM 1916 O HOH A 243 11.793 23.332 13.260 1.00 19.06
.000
ATOM 1917 HW1 HOH A 243 12.609 23.332 13.837 1.00 0.00
ATOM 1918 HW2 HOH A 243 10.977 23.332 13.837 1.00 0.00
END
Any guidance you could provide would be appreciated.
Thanks, Marc
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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