Ilya Chorny wrote:
I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached
to the side chain nitrogen called ASBG. I want to test the new residue
by itself.
When I pdb2gmx it I get the following error.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.3
Source code file: pgutil.c, line: 87
Fatal error:
Atom N not found in residue 1094904186 while adding improper
-------------------------------------------------------
If the residue is by itself, something is seriously wrong if pdb2gmx is
detecting a billion residues!
If I comment out
CA +N C O improper_O_C_X_Y
Right, because if the residue is by itself, there will be no N in the next
residue (+N).
Then pdb2gmx creates the gro and top with no error messages.
I saw an much earlier post by Justin with a similar error message but no
resolution. Anyone have anythoughts?
IIRC, that was in reference to version 3.3.1, which turned out to be the result
of a broken Ubuntu package, and was not a problem with Gromacs itself.
Try it in the context of the actual molecule, if topology construction requires
the next residue. In isolation, that residue will always fail with +N.
-Justin
Thanks,
Ilya
--
Ilya Chorny Ph.D.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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