[gmx-users] multple T-coupling errors

[Yunhong Hotta]

Hi, all 

I just run the MD run of a protein without deleting the crystallographic
water. When i go for grompp with positional restraint, I get an fatal
error  as:

Fatal error:Atom 3176 in multple T-coupling groups(13 and 1)

Where the atom 3176 corresponds to the last atom of the ligand. 

I check up the mailing list and know that i have some error in my .mdp file.
But i don`t know how can i fix it. 

The tail of .top is :
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
SOL               143
SOL             4318

The contents of .mdp is :
[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
SOL               143
SOL             4318
[root at dhcp040 ~]# cat PR.mdp
title               =  PR
warnings            =  10
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  1000     ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10
nstvout             =  100
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1              0.1             0.1
tc-grps             =  protein          sol             sol
ref_t               =  300              300             300
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

Can anyone suggest me how can I fix this error?

Thank you for your time !

Yunhong Hotta ( Research Assitant )
email : 4yunhong at bunshi3.bio.naogya-u.ac.jp
Division of biological science
Graduate School of Science
Nogoya University 
Japan