DimitryASuplatov wrote:
Hello,
thanks for the tip about -pname flag for genion - that was the problem in the
first place.
While I was waiting for the reply I set -maxwarn=1 and ran the simulation. At
the end I got the gro file with the following lines
. . . .
31598SOL OW 5239 7.367 10.098 9.759 -0.9983 -0.8372 -0.3184
31598SOL HW1 5240 7.442 10.103 9.693 -0.1595 -1.8795 0.4694
31598SOL HW2 5241 7.280 10.115 9.713 -0.2726 1.4897 -1.0786
31599NA+ NA 5242 9.240 1.342 5.490 0.0506 0.7314 0.4913
31600NA+ NA 5243 1.452 0.891 5.672 0.0663 -0.3132 -0.0275
31601NA+ NA 5244 0.332 0.852 10.563 -0.4915 -0.6099 0.0614
. . . .
31679CL- CL 5322 1.332 0.993 10.254 -0.1729 -0.0048 -0.2991
31680CL- CL 5323 0.142 3.208 2.770 0.2592 0.3646 0.0936
31681CL- CL 5324 0.681 2.561 5.594 -0.0556 0.0660 0.1265
31682CL- CL 5325 0.112 3.607 8.225 0.1200 -0.0190 0.0017
. . . .
I guess this names are OK - grompp has taken them from top file to replace old
gro names.
Well, in the case of ions, this is probably harmless. But do be aware that this
particular warning from grompp is useful in the case of (for example) small
molecules in solution with a protein. If the order of the .top and .gro don't
match, then grompp will give you the same complaint, in which case it is *not*
safe to proceed without properly resolving the issue.
-Justin
SDA
--
========================================
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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