<br><br><div class="gmail_quote">On 17 June 2011 10:23, ITHAYARAJA <span dir="ltr"><<a href="mailto:ithayaraja@gmail.com">ithayaraja@gmail.com</a>></span> wrote:<br><div><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Sir,<br>Above error was solved but the system has raised a following new error, i.e.,<br><br>Fatal error:<br>52 atoms are not part of any of the T-Coupling groups<br><br>How do I find which atom file has problem?<br>
help me to solve this problem...........<br>
<br><br clear="all"><br></blockquote><div>My position restraint parameter file is <br><br>title = cpeptide position restraining
<br>warnings = 10
<br>cpp = C:\Program Files\CTCBioapps\gromacs3.3\cpp.exe
<br>define = -DPOSRES
<br>constraints = all-bonds
<br>integrator = md
<br>dt = 0.002 ; ps ! <br>nsteps = 10000 ; total 20.0 ps. <br>nstcomm = 1
<br>nstxout = 250 ; output coordinates every 0.5 ps <br>nstvout = 1000 : output velocities every 2.0 ps <br>nstfout = 0
<br>nstlog = 10
<br>nstenergy = 10
<br>nstlist = 10
<br>ns_type = grid
<br>rlist = 1.0
<br>coulombtype = PME <br>rcoulomb = 1.0
<br>rvdw = 1.0
<br>fourierspacing = 0.12 <br>fourier_nx = 0 <br>fourier_ny = 0 <br>fourier_nz = 0 <br>pme_order = 6 <br>ewald_rtol = 1e-5 <br>optimize_fft = yes <br>; Berendsen temperature coupling is on in three groups
<br>Tcoupl = berendsen
<br>tau_t = 0.1 0.1 0.1 0.1 0.1 <br>tc-grps = protein sol FAD NDP GSH <br>ref_t = 300 300 300 300 300 <br>; Pressure coupling is not on
<br>Pcoupl = no
<br>pcoupltype = isotropic <br>tau_p = 0.5
<br>compressibility = 4.5e-5
<br>ref_p = 1.0
<br>; Generate velocites is on at 300 K.
<br>gen_vel = yes
<br>gen_temp = 310.15
<br>gen_seed = 173529/n<br></div></div><br clear="all"><br>-- <br><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>
Tamil Nadu<br>India<br>