Dear, <div> I am working in complex protein which contains one ligand and one Mg2+ ion. I am got an error while running grompp for NVT. </div><div><br></div><div>grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr </div>
<div><br></div><div><div style>---------------------------------------------------------------------------------------</div><div style>Program grompp, VERSION 4.5.3</div><div style>Source code file: readir.c, line: 1402</div>
<div style><br></div><div style>Ftal error:</div><div style>1 atoms are not part of any of the T-Coupling groups</div><div style>------------------------------------------------------------------------------------------</div>
<div style><br></div><div style>For creating the index file before grompp i used the following command</div><div style><pre style="white-space:pre-wrap">make_ndx -f em.gro -o index.ndx</pre></div><div style><div> 0 System : 248986 atoms</div>
<div> 1 Protein : 5019 atoms</div><div> 2 Protein-H : 3975 atoms</div><div> 3 C-alpha : 519 atoms</div><div> 4 Backbone : 1557 atoms</div><div> 5 MainChain : 2077 atoms</div>
<div> 6 MainChain+Cb : 2556 atoms</div><div> 7 MainChain+H : 2575 atoms</div><div> 8 SideChain : 2444 atoms</div><div> 9 SideChain-H : 1898 atoms</div><div> 10 Prot-Masses : 5019 atoms</div>
<div> 11 non-Protein : 243967 atoms</div><div> 12 Other : 24 atoms</div><div> 13 <span class="il" style="background-image:initial;background-color:rgb(255,255,204)">MG2+</span> : 1 atoms</div>
<div> 14 UNK : 23 atoms</div><div> 15 NA : 1 atoms</div><div> 16 Water : 243942 atoms</div><div> 17 SOL : 243942 atoms</div><div> 18 non-Water : 5044 atoms</div>
<div> 19 Ion : 1 atoms</div><div> 20 <span class="il" style="background-image:initial;background-color:rgb(255,255,204)">MG2+</span> : 1 atoms</div><div> 21 UNK : 23 atoms</div>
<div> 22 NA : 1 atoms</div><div> 23 Water_and_ions : 243943 atoms</div><div><br></div><div> nr : group ! 'name' nr name 'splitch' nr Enter: list groups</div><div> 'a': atom & 'del' nr 'splitres' nr 'l': list residues</div>
<div> 't': atom type | 'keep' nr 'splitat' nr 'h': help</div><div> 'r': residue 'res' nr 'chain' char</div><div> "name": group 'case': case sensitive 'q': save and quit</div>
<div> 'ri': residue index</div><div><br></div><div>> 1 | 14</div><div><br></div><div>Copied index group 1 'Protein'</div><div>Copied index group 14 'UNK'</div><div>Merged two groups with OR: 5019 23 -> 5042</div>
<div><br></div><div> 24 Protein_UNK : 5042 atoms</div><div><br></div><div>> q</div></div><div style><br></div><div style><br></div><div style>nvt.mdp i used</div><div style><br></div><div style><div><font color="#222222" face="arial, sans-serif">title = Protein-ligand complex NVT equilibration </font></div>
<div><font color="#222222" face="arial, sans-serif">define = -DPOSRES </font></div><div><font color="#222222" face="arial, sans-serif">integrator = md </font></div><div><font color="#222222" face="arial, sans-serif">nsteps = 50000 </font></div>
<div><font color="#222222" face="arial, sans-serif">dt = 0.002 </font></div><div><font color="#222222" face="arial, sans-serif">nstxout = 100 </font></div><div><font color="#222222" face="arial, sans-serif">nstvout = 100 </font></div>
<div><font color="#222222" face="arial, sans-serif">nstenergy = 100 </font></div><div><font color="#222222" face="arial, sans-serif">nstlog = 100 </font></div><div><font color="#222222" face="arial, sans-serif">energygrps = Protein UNK</font></div>
<div><font color="#222222" face="arial, sans-serif">continuation = no </font></div><div><font color="#222222" face="arial, sans-serif">constraint_algorithm = lincs </font></div><div><font color="#222222" face="arial, sans-serif">constraints = all-bonds </font></div>
<div><font color="#222222" face="arial, sans-serif">lincs_iter = 1 </font></div><div><font color="#222222" face="arial, sans-serif">lincs_order = 4 </font></div><div><font color="#222222" face="arial, sans-serif">ns_type = grid </font></div>
<div><font color="#222222" face="arial, sans-serif">nstlist = 5 </font></div><div><font color="#222222" face="arial, sans-serif">rlist = 0.9 </font></div><div><font color="#222222" face="arial, sans-serif">rcoulomb = 0.9 </font></div>
<div><font color="#222222" face="arial, sans-serif">rvdw = 1.4 </font></div><div><font color="#222222" face="arial, sans-serif">coulombtype = PME </font></div><div><font color="#222222" face="arial, sans-serif">pme_order = 4 </font></div>
<div><font color="#222222" face="arial, sans-serif">fourierspacing = 0.16 </font></div><div><font color="#222222" face="arial, sans-serif">tcoupl = V-rescale </font></div><div><font color="#222222" face="arial, sans-serif">tc-grps = Protein_UNK Water_and_ions </font></div>
<div><font color="#222222" face="arial, sans-serif">tau_t = 0.1 0.1 </font></div><div><font color="#222222" face="arial, sans-serif">ref_t = 300 300 </font></div><div><font color="#222222" face="arial, sans-serif">pcoupl = no </font></div>
<div><font color="#222222" face="arial, sans-serif">pbc = xyz </font></div><div><font color="#222222" face="arial, sans-serif">DispCorr = EnerPres </font></div><div><font color="#222222" face="arial, sans-serif">; Velocity generation</font></div>
<div><font color="#222222" face="arial, sans-serif">gen_vel = yes </font></div><div><font color="#222222" face="arial, sans-serif">gen_temp = 300 </font></div><div><font color="#222222" face="arial, sans-serif">gen_seed = -1 </font></div>
</div><div style><br></div><div style>I am not clear how i can add MG2+ while creating index.ndx file. Please help me out. </div></div><div><br></div><div> </div><div>P.Kalaiarasan<div>National Centre of Applied Human Genetics</div>
<div>School of Life Sciences</div><div>JNU</div><div>New Delhi</div><div>India</div><br>
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