[gmx-users] dummy atom definition prob in FEP

[Wang Qin]

Hi there,
        I have a problems when I do a FEP calculation.
        Below is how I defined dummy atoms in the topology file:
[atom]
;nr     type            resnr   residue atom    cgnr    charge
mass            type_B  charge_B        mass_B
21      opls_172        1       LG6     H21     21      0.4650  1.00800
opls_0          0.0000  0.000000
22      opls_172        1       LG6     H22     22      0.4650  1.00800
opls_0          0.0000  0.000000
......

[virtual_sites3]
;Site from from from funct theta d
21      10      2       1       3       108      0.09450
22      11      4       3       3       108     0.09450

[bonds]
...

      The problem is when I ran grompp, there are 2 fatal errors, saying:
ERROR 1:
  virtual site H21 (Res LG6-173) has non-zero mass 1.008
       Check your topology.

ERROR 2:
  virtual site H22 (Res LG6-173) has non-zero mass 1.008
       Check your topology.

-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source code file: grompp.c, line: 1180

Fatal error:
There were 2 errors in input file(s)
-------------------------------------------------------


Does anyone know anything about it? Is there any mistake I made? How should
I do? Thank you very much.

Regards,
Qin
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