Hi there,<br>
I have a problems when I do a FEP calculation. <br>
Below is how I defined dummy atoms in the topology file:<br>
[atom]<br>
;nr
type
resnr residue atom cgnr
charge
mass
type_B charge_B mass_B<br>
21
opls_172
1 LG6
H21 21
0.4650 1.00800
opls_0
0.0000 0.000000<br>
22
opls_172
1 LG6
H22 22
0.4650 1.00800
opls_0
0.0000 0.000000<br>
......<br>
<br>
[virtual_sites3]<br>
;Site from from from funct theta d<br>
21 10
2
1
3 108
0.09450<br>
22 11
4
3
3 108
0.09450<br>
<br>
[bonds]<br>
...<br>
<br>
The problem is when I ran grompp, there are 2 fatal errors, saying: <br>
ERROR 1:<br>
virtual site H21 (Res LG6-173) has non-zero mass 1.008<br>
Check your topology.<br>
<br>
ERROR 2:<br>
virtual site H22 (Res LG6-173) has non-zero mass 1.008<br>
Check your topology.<br>
<br>
-------------------------------------------------------<br>
Program grompp_mpi, VERSION 3.3.1<br>
Source code file: grompp.c, line: 1180<br>
<br>
Fatal error:<br>
There were 2 errors in input file(s)<br>
-------------------------------------------------------<br>
<br>
<br>
Does anyone know anything about it? Is there any mistake I made? How should I do? Thank you very much.<br>
<br>
Regards,<br>
Qin