What's happening is that grompp is reaching the end of your topology
(line 998) and identifying what it thinks is a problem. I'm guessing
your peptide has 155 atoms? Using Protein Non-protein is fine, and is
the best thing to do in this scenario. The warning is really meant to
alert individuals who do something like:
tc-grps = Protein SOL NA+ CL-
which is destined for problems.
I'd say everything you've done is fine.
-Justin
Serena Leone wrote:
Hello everybody,
I am trying to run a high temperature "rough" dynamic on a polypeptide
to randomize its structure. When I pre-process the structure in the
solvent I get the " T-Coupling group XXX has fewer than 10% of the
atoms" error. This error is also described in the wiki and suggests to
couple the groups "Protein" and "non-Protein", which I actually did.
The error message that I get is:
processing index file...
WARNING 1 [file "H1.top", line 998]:
T-Coupling group Protein has fewer than 10% of the atoms (155 out of
29508)
Maybe you want to try Protein and Non-Protein instead?
Making dummy/rest group for Acceleration containing 29508 elements
Making dummy/rest group for Freeze containing 29508 elements
Making dummy/rest group for Energy Mon. containing 29353 elements
Making dummy/rest group for VCM containing 29508 elements
Number of degrees of freedom in T-Coupling group Protein is 464.98
Number of degrees of freedom in T-Coupling group Non-Protein is 58710.02
Making dummy/rest group for User1 containing 29508 elements
Making dummy/rest group for User2 containing 29508 elements
Making dummy/rest group for XTC containing 29508 elements
Making dummy/rest group for Or. Res. Fit containing 29508 elements
Making dummy/rest group for QMMM containing 29508 elements
T-Coupling has 2 element(s): Protein Non-Protein
Energy Mon. has 2 element(s): Protein rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
but as you can see, the groups are assigned. Beside, line 998 in my
.top is the line referring to the Cl ions:
993 [ molecules ]
994 ; Compound #mols
995 Protein_A 1
996 SOL 9782
997 NA+ 1
998 CL- 6
but I thought the T-coupling groups were defined in the index file,
not the topology. Anybody knows what I am doing wrong?
Thanks a lot
Serena
--
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
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========================================
Justin A. Lemkul
Graduate Research Assistant
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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