<DIV id=RTEContent>Dear sir : how can you produce distance itp file? Thank you in advance!<BR><BR><B><I>Tsjerk Wassenaar <tsjerkw@gmail.com></I></B> 写道： <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Misha,<BR><BR>You can only apply distance restraints within one molecule, so the workaround is to put the desired SOL molecule in the .itp file (and change the order in the .gro file accordingly).<BR><BR>Hope it helps,<BR><BR>Tsjerk<BR><BR> <DIV><SPAN class=gmail_quote>On 11/19/05, <B class=gmail_sendername>Иванов Миша</B> <<A href="mailto:grasp2@mail.ru">grasp2@mail.ru</A>> wrote:</SPAN> <BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><BR>Dear users,<BR><BR>I would like to make a distance restraints. I create a file "disres.itp" with the following content:<BR>[ distance_restraints
]<BR>; ai aj type index type low up1 up2 fac <BR> 3177 3906 1 1 1 0.0 0.3 0.7 1<BR>where the first atom is form "chain A" of my system and the second is from "SOL".<BR>My question is:<BR>What command should I untroduce in .top file and in what part of it, to make Grompp understand that the first atom is from CHAIN A and the second - from Solvent. <BR>My top file is written below.<BR><BR>Sicerely yours,<BR>Misha Ivanov<BR><BR>; This is your topology file<BR>; ?<BR>;<BR>; Include forcefield
parameters<BR>#include "ffgmx.itp"<BR><BR>; Include chain topologies <BR>#include "1_A.itp"<BR>#include "1_B.itp"<BR><BR>; Include water topology<BR>#ifdef FLEX_SPC<BR>#include "flexspc.itp"<BR>#else<BR>#include "spc.itp"<BR>#endif<BR><BR>#ifdef POSRES_WATER <BR>; Position restraint for each water oxygen<BR>[ position_restraints ]<BR>; i funct fcx fcy fcz<BR> 1 1 1000 1000 1000<BR>#endif<BR><BR>[ system ]<BR>; Name<BR>?<BR><BR>[ molecules ] <BR>; Compound #mols<BR>Protein_A 1<BR>Protein_B
1<BR>SOL 223<BR><BR><BR><BR>_______________________________________________<BR>gmx-users mailing list<BR><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</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>_______________________________________________<BR>gmx-users mailing
list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE><BR></DIV><p>
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