[gmx-developers] Amber ions.itp

[Alexey Shvetsov]

Hi all!

Seems current implentation of amber.ff in gromacs has missing ions
masses in ions.itp

Warning: atom name 12328 in speptide.top and
speptide.ions.gro does not match (Na - NA)
Warning: atom name 12329 in
speptide.top and speptide.ions.gro does not match (Na - NA)
Warning: atom
name 12330 in speptide.top and speptide.ions.gro does not match (Ca -
CL)
Warning: atom name 12331 in speptide.top and speptide.ions.gro does not
match (Ca - CL)

WARNING 1 [file speptide.top, line 2704]:
  4 non-matching
atom names
  atom names from speptide.top will be used
  atom names from
speptide.ions.gro will be ignored


double-checking input for internal
consistency...
renumbering atomtypes...
converting bonded
parameters...

ERROR 1 [file speptide.top, line 2704]:
  atom Na (Res Na+-1)
has mass 0



ERROR 2 [file speptide.top, line 2704]:
  atom Ca (Res Cl--1)
has mass 0



There was 1 warning

-- 
Best Regards,
Alexey 'Alexxy'
Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of
Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux
Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pn
pi.spb.ru
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