Ilya Chorny wrote:
On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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!
I'll checkmy file again.
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).
If this is true then pdb2gmx will crash evertime it is run on an
isolated AA, which it doesn't.
Not if pdb2gmx recognizes how to treat termini. If you are using non-standard
residues and creating new linkages between polymers, then you may encounter
problems. Perhaps the problem relates the actual residue itself, have you added
ASBG to aminoacids.dat? You haven't showed us your pdb2gmx command line, so we
can only assume that something is not being done correctly.
-Justin
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Ilya Chorny Ph.D.
--
========================================
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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