[gmx-users] Problems with ion names in OPLS and gromacs 4.0.2

[Justin A. Lemkul]

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
> 
> 

-- 
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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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