On 5/3/12 12:32 PM, kalai arasan wrote:
Dear,
I am working in complex protein which contains one ligand and one Mg2+
ion. I am got an error while running grompp for NVT.
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
---------------------------------------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: readir.c, line: 1402
Ftal error:
1 atoms are not part of any of the T-Coupling groups
------------------------------------------------------------------------------------------
For creating the index file before grompp i used the following command
make_ndx -f em.gro -o index.ndx
0 System : 248986 atoms
1 Protein : 5019 atoms
2 Protein-H : 3975 atoms
3 C-alpha : 519 atoms
4 Backbone : 1557 atoms
5 MainChain : 2077 atoms
6 MainChain+Cb : 2556 atoms
7 MainChain+H : 2575 atoms
8 SideChain : 2444 atoms
9 SideChain-H : 1898 atoms
10 Prot-Masses : 5019 atoms
11 non-Protein : 243967 atoms
12 Other : 24 atoms
13 MG2+ : 1 atoms
14 UNK : 23 atoms
15 NA : 1 atoms
16 Water : 243942 atoms
17 SOL : 243942 atoms
18 non-Water : 5044 atoms
19 Ion : 1 atoms
20 MG2+ : 1 atoms
21 UNK : 23 atoms
22 NA : 1 atoms
23 Water_and_ions : 243943 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 1 | 14
Copied index group 1 'Protein'
Copied index group 14 'UNK'
Merged two groups with OR: 5019 23 -> 5042
24 Protein_UNK : 5042 atoms
> q
nvt.mdp i used
title = Protein-ligand complex NVT equilibration
define = -DPOSRES
integrator = md
nsteps = 50000
dt = 0.002
nstxout = 100
nstvout = 100
nstenergy = 100
nstlog = 100
energygrps = Protein UNK
continuation = no
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = Protein_UNK Water_and_ions
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
pbc = xyz
DispCorr = EnerPres
; Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = -1
I am not clear how i can add MG2+ while creating index.ndx file. Please help me
out.
Three approaches:
1. Create a group that replaces "Water_and_ions" with one that contains the MG2+
ion within the solvent
2. Add MG2+ to residuetypes.dat so that it is recognized as an ion
3. Couple the MG2+ and protein/ligand together, as might make the most physical
sense
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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