Hello!
I would like to involve formate molecule (HCOO-)in my dynamics, but I have the
problem when I use virtual site (type 3fd)for it.
When I run grompp for single formate molecule, it`s ok.
But after solvating in bath of solvent (tip3p) grompp runs with error:
Cleaning up constraints and constant bonded interactions with virtual sites
Removed 1 Proper Dih.s with virtual sites, 0 left
Converted 1 Constraints with virtual sites to connections, 2 left
ERROR: Cannot have constraint (5-1) with virtual site (1)
ERROR: Cannot have constraint (8-1) with virtual site (1)
ERROR: Cannot have constraint (11-1) with virtual site (1)
ERROR: Cannot have constraint (14-1) with virtual site (1)
..........................................
ERROR: Cannot have constraint (3101-1) with virtual site (1)
ERROR: Cannot have constraint (3104-1) with virtual site (1)
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: vsite_parm.c, line: 686
Fatal error:
There were 1034 virtual sites involved in constraints
-------------------------------------------------------
And 1034 is number of water molecules. In my mdp file the line that corresponds
to constraints is
"constraints = none". This is my topology:
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
FMT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_279 1 FMT H 1 0.22 0 ; qtot
0.22
2 opls_271 1 FMT C 1 0.58 13.019 ; qtot 0.8
3 opls_272 1 FMT O1 1 -0.9 15.9994 ; qtot
-0.1
4 opls_272 1 FMT O2 1 -0.9 15.9994 ; qtot -1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
2 4 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 ang_FMT_H_C_O1
1 2 4 1 ang_FMT_H_C_O2
3 2 4 1 ang_FMT_O1_C_O2
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
1 3 2 4 1 improper_O_C_X_Y
[ virtual_sites3 ]
; ai aj ak al funct c0 c1
1 2 3 4 2
; Include water topology
#include "tip3p.itp"
[ system ]
; Name
FMT in water
[ molecules ]
; Compound #mols
FMT 1
SOL 1034
Could You help me to solve this roblem!
Thanks!
_____________
Dmitri Nilov
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