DimitryASuplatov wrote:
Hello,
I want neutralize negative charge in my structure. I use genion to add
80 Na and 71 Cl. Than I edit top file manually to decrease SOL number by
151 and add two lines for ions. Since I use OPLSAA they should look like
this (considering names in gromacs/share/gromacs/top/ions.itp)
NA+ 80
CL- 71
When I run grompp afterwards I receive this message:
--------------------------------------------------------
Warning: atom name 105260 in 1klc_final_frc.top and
1klc_final_frc.si.gro does not match (NA - Na)
Warning: atom name 105261 in 1klc_final_frc.top and
1klc_final_frc.si.gro does not match (NA - Na)
(more than 20 non-matching atom names)
WARNING 1 [file 1klc_final_frc.top, line 42]:
151 non-matching atom names
atom names from 1klc_final_frc.top will be used
atom names from 1klc_final_frc.si.gro will be ignored
--------------------------------------------------------
That was expected since gro file identifies the ions as "Na" and "Cl",
but this is the first time in my experience when grompp throws out this:
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: gmx_fatal.c, line: 481
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------
Is this a problem or should I simply set -maxwarn to 2?
What was your genion command line? Did you specify, i.e. genion -pname Na
-nname Cl? The names you give genion should match the atom names you find in
ions.itp, which for OPLS should be NA+ and CL- (Na and Cl are for ffgmx).
-Justin
Thanks. I appreciate your time.
SDA
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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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