[gmx-users] Re: invalid line (coordinates)

[sarah k]

dear Justin,

The link of (http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology)
helped but still I have problem.

There are 35344SOL molecules in my _solv.gro file. the last atom is N2
72342. The last part of my topol.top file is:
[molecules]
; compound               #mols
Protein_A                         1
Protein_B                         1
Protein_C                         1
Protein_D                         1
SOL                          27363
NA+                                 0

Then typing grompp commands gives:
number of coordinates in coordinate file (a_solv.gro, 72342) does not
match (topol.top, 72341)

I guess that the topol.top is based on water not matching nitrogen
that is why I can't balance the numbers.

I also tried to run again from the begining on my case protein. this
time I manipulated the topol file with these numbers:
[molecules]
; compound               #mols
Protein_A                         1
SOL                          24044
NA+                                 1

It started operating but:
note: System has non-zero total charge: -1.000000e+00 (which is quite logical)
warning: atom name 210 in topol.top and a_solv.gro does not match (OW- N)
......
WARNING 1 [file topol.top, line 37]: 72133 non matching atom names
atom names from topol.top will be used
atom names from a_solv.gro will be ignored

Does it mean that it will replace the nitrogen solvent with water
molecules? What should I do this time? Thanks.

Best regards,
Sarah