Nilesh Dhumal wrote:
I have addes the "CO" residue.
Coordinate file
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010
HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C
HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00 O
HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00 O
END
in ffopla.rtp file.
[ CO ] ; mandatory
[ ATOMS ] ; mandatory
C1 opls_974 1.00 1
O2 opls_975 -0.50 2
O3 opls_976 -0.50 2
[ bonds ]
C1 O2
C1 O3
I have also addes new atoms typs in ffopls.atp file.
These input files work fine for me. The error message complained about an atom
named "O" so be sure you're using the input you think you are. Something has
gotten confused somewhere.
-Justin
NIlesh
On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am getting the following error during pdb2gmx.
Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms
while sorting atoms
I checked the pdb file and ffopls.rtp file also.
And what did you find? To my knowledge there is no such residue "CO" in
the ffoplsaa.rtp file. Is this something you've added? Regardless,
there's a mismatch somewhere, so if you can't identify it, post the text
of your coordinate file and the relevant .rtp entry to see if someone else
can spot it.
-Justin
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
MILES-IGERT Trainee
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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