Have a look at the rtp file of the force field u r using for correct representation of the ion used..<br><br clear="all">With regards,<br> J. John Wesly,<br> FInal Year, B.Tech., Bioinformatics,<br> School of Chemical and Biotechnology, <br>
SASTRA University, Thanjavur,<br> Tamil Nadu, India.<br><br><~WesFaith~><br>"He who desire to learn, pursues towards edification... One who has will to do, finds a way how to do.<br> Have a LEARNING SPREE.... Desire to learn... Passion to know things... Unravel the mysteries about your abilities... "<br>
<br><br><div class="gmail_quote">On Sun, Dec 26, 2010 at 12:26 PM, shikha agarwal <span dir="ltr"><<a href="mailto:shikhaiiitabi@gmail.com">shikhaiiitabi@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
hello ,<br><br>this is my ions.itp file for gromos53a6 forcefield<br><br>[ moleculetype ]<br>; molname nrexcl<br>CU1 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>
1 CU1+ 1 CU1 CU 1 1 63.54600<br><br>[ moleculetype ]<br>; molname nrexcl<br>CU 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CU2+ 1 CU CU 1 2 63.54600<br>
<br>[ moleculetype ]<br>; molname nrexcl<br>ZN 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 ZN2+ 1 ZN ZN 1 2 65.37000<br>this is my ions.itp<br>
<br>[ moleculetype ]<br>; molname nrexcl<br>MG 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 MG2+ 1 MG MG 1 2 24.30500<br><br>
[ moleculetype ]<br>; molname nrexcl<br>CA 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CA2+ 1 CA CA 1 2 40.08000<br><br>[ moleculetype ]<br>
; molname nrexcl<br>NA 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 NA+ 1 NA NA 1 1 22.9898<br><br>[ moleculetype ]<br>; molname nrexcl<br>
CL 1<br><br>[ atoms ]<br>; id at type res nr residu name at name cg nr charge mass<br>1 CL- 1 CL CL 1 -1 35.45300<br><br><br><br><br>for adding ions I used this command ...<br>
<br>genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 -nname CL-<br><br>now when I m doing EM then getting this error <br><br>grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr<br>
<br>Fatal error:<br>No such moleculetype NA+<br><br><br>help me !<br><br>regards:<br><font color="#888888">shikha<br><br>
</font><br>--<br>
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