Hi :)<br><br>Not the box, you probably need NA or NA+. It's case sensitive and depends on the force field definition you use. <br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 4/5/06, <b class="gmail_sendername">
Adriana Pietropaolo</b> <<a href="mailto:adriana@ms.fci.unibo.it">adriana@ms.fci.unibo.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Probably you generated a bad box.<br>Check the box with i.e. rasmol and try to use -princ option in editconf<br>(to put the protein in its inertial axes) and genion to make the ions to<br>ensure charge neutrality.<br>good luck,
<br>Adriana<br><br>> hi<br>> today i have tried with some other protein but the problem still persists .<br>> today i will tell you problem in detail<br>><br>> today i have taken the protein pdb file which conatains only the amino
<br>> acids no hetero atoms<br>><br>> i have run the pdb2gmx command<br>> pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n<br>> 1/out1.ndx -q 1/out1.pdb<br>><br>> i got all the 5 files<br>
><br>> later i used the command edit conf<br>> editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7<br>><br>> then i run the genbox<br>> genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out
1.top<br>> here i got the gro file and modified top file<br>><br>> then i have run the grompp<br>> grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr<br>> my mdp file is<br>> bellow<br>><br>
> ##########################################################<br>> title = drg_trp<br>> cpp = /usr/bin/cpp<br>> define = -DFLEX_SPC<br>> constraints = none
<br>> integrator = steep<br>> dt = 0.002 ; ps !<br>> nsteps = 1000<br>> ns_type = grid<br>> rlist = 0.9<br>> coulombtype = PME ; Use particle-mesh ewald
<br>> rcoulomb = 0.9<br>> rvdw = 1.0<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4
<br>> ewald_rtol = le-5<br>> optimize_fft = yes<br>> Tcoupl = no<br>> Pcoupl = no<br>> gen_vel = no<br>> ;<br>> ; Energy minimizing stuff
<br>> ;<br>> emtol = 1000.0<br>> emstep = 0.01<br>> ###############################################################<br>> There i got one NOTE : System has non-zero total charge: -
6.999998e+00<br>><br>> later i tried to run the mdrun but the process fails at 24 steps<br>><br>> Then i used the genion<br>><br>> genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log<br>>
<br>> here i got the modified gro file<br>> but tere was warning that<br>> turning of free energy, will use lambda=0<br>> Then i have edited the top file i got according to the gro file<br>> since i m using the gromacs
3.3 the #include ions.itp was default<br>> so i have removed the 7 water atoms from the top file and added 7 Na atoms<br>> and run the grompp<br>><br>> grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
<br>> here the programme was failed showing the error<br>> Fatal error:<br>> No such moleculetype Na<br>> i have checked the ions .itp<br>> its having the information Na atom than why its showing this i could
<br>> n't understand<br>> can any one help me over this here i have attatched my out6.gro file<br>> and the top file<br>><br>> Thanking you<br>> Santosh Naik<br>> _______________________________________________
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http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br>--<br>_____________________________________________<br>Adriana Pietropaolo,<br>PhD student,<br>dipartimento di Chimica Fisica ed Inorganica,<br>Facolta' di Chimica Industriale
<br>Universita' di Bologna<br>WEB:<a href="http://www2.fci.unibo.it/~adriana">www2.fci.unibo.it/~adriana</a><br>Tel 051/6446992<br>FAX 051/2093690<br>_____________________________________________<br><br><br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>