Jack Shultz wrote:
On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Jack Shultz wrote:
<snip>
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom O in residue CARG 244 not found in rtp entry with 25 atoms
while sorting atoms
-------------------------------------------------------
But we got an O here
ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00
O
The error is not telling you that the O atom is missing from the .pdb file;
it is telling you that it is present in the .pdb, but not in the .rtp entry.
Look at the .rtp entry for CARG
[ CARG ]
[ atoms ]
N amber99_34 -0.34810 1
H amber99_17 0.27640 2
CA amber99_11 -0.30680 3
HA amber99_19 0.14470 4
CB amber99_11 -0.03740 5
HB1 amber99_18 0.03710 6
HB2 amber99_18 0.03710 7
CG amber99_11 0.07440 8
HG1 amber99_18 0.01850 9
HG2 amber99_18 0.01850 10
CD amber99_11 0.11140 11
HD1 amber99_19 0.04680 12
HD2 amber99_19 0.04680 13
NE amber99_38 -0.55640 14
HE amber99_17 0.34790 15
CZ amber99_3 0.83680 16
NH1 amber99_38 -0.87370 17
HH11 amber99_17 0.44930 18
HH12 amber99_17 0.44930 19
NH2 amber99_38 -0.87370 20
HH21 amber99_17 0.44930 21
HH22 amber99_17 0.44930 22
C amber99_2 0.85570 23
OC1 amber99_45 -0.82660 24
OC2 amber99_45 -0.82660 25
- you should have an O1 and O2 atom for the
I made the following modification
ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O
ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O
Forgive my typo, what I meant was OC1 and OC2. You must always make sure the
atoms in the structure file match those expected by the .rtp file. You need OC1
and OC2.
-Justin
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom O in residue CARG 122 not found in rtp entry with 25 atoms
while sorting atoms
-------------------------------------------------------
C-terminal carboxylate.
-Justin
--
========================================
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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--
========================================
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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