nicegromacs wrote:
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
but when I add one more repetitive unit (H-R-R-T) I get the following
error:
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can you post
the .pdb file?
-Justin
"Stop Drinking My Beer !" (The Amps)
nicegromacs wrote:
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
one terminus of your polymer chain. You may find this post useful:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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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