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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