On 1/2/13 7:15 AM, James Starlight wrote:
Justin,
so why my simulation of the sp3 lattice have been crashed with the
links warnings ( which always tells about wrong geometry in topology)?
Incorrect geometry is not the only cause of LINCS warnings. I haven't seen
nearly enough information to know what the cause of the problem is.
also I've tried to paraetrize completely planar (sp2) lattice but
obtain errors like that
Can not find forcefield for atom C27-22 with 2 bonds
Can not find forcefield for atom C28-23 with 3 bonds
Can not find forcefield for atom C4-24 with 3 bonds
Can not find forcefield for atom C15-25 with 3 bonds
Can not find forcefield for atom C1-26 with 3 bonds
Can not find forcefield for atom C39-27 with 3 bonds
Can not find forcefield for atom C41-28 with 3 bonds
Can not find forcefield for atom C30-29 with 3 bonds
Can not find forcefield for atom C2-30 with 2 bonds
Can not find forcefield for atom C5-31 with 2 bonds
Can not find forcefield for atom C8-32 with 3 bonds
Can not find forcefield for atom H22-33 with 0 bonds
So I've decided that the atom names is also relevant besides the
geometry which was correct in that case.
No, the names don't matter. The program is simply telling you that you have
some atoms that don't fit within the criteria of existing .n2t entries. You may
have to write your own in order for the program to complete successfully. The
H22 atom is particularly instructive - it says zero bonds, which means that it
is not within the distance cutoff to be actually bonded to anything.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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