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<TD>Dear Mark Abraham,<br ><br >I have changed MeoH to SOL in .gro and .itp files and also changed the #include line to "methanol.itp"<br >It now seemed to have written the solvent molecules in the top file with SOL as the name with atom types of methanol. <br >When I ran grompp program as following I get the error as shown below: I am also attaching the .gro,.itp,.top files. for information. Did I miss out anything ? <br ><SPAN STYLE="font-weight: bold; font-style: italic;">grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr<br ><br >[asd@ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr<br > <br ></SPAN><font size="2" face="Arial"><SPAN STYLE="font-weight: bold; font-style: italic;"> Option Type Value Description<br > ------------------------------------------------------<br > -[no]h bool no Print help info and quit<br > -[no]X bool no Use dialog box GUI to edit command line options<br > -nice int 0 Set the nicelevel<br > -[no]v bool yes Be loud and noisy<br > -time real -1 Take frame at or first after this time.<br > -np int 1 Generate statusfile for # nodes<br > -[no]shuffle bool no Shuffle molecules over nodes<br > -[no]sort bool no Sort molecules according to X coordinate</SPAN></font><br ><SPAN STYLE="font-weight: bold; font-style: italic;"><br >creating statusfile for 1 node...<br ><br >Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#<br >checking input for internal consistency...<br >calling /lib/cpp...<br >processing topology...<br >Generated 141 of the 1176 non-bonded parameter combinations<br >Excluding 3 bonded neighbours for Protein 1<br >Cleaning up temporary file grompp5RBSRX<br >-------------------------------------------------------<br >Program grompp, VERSION 3.3<br >Source code file: toppush.c, line: 1264<br ><br >Fatal error:<br >No such moleculetype SOL<br >-------------------------------------------------------<br ><br ></SPAN>I never prefer working in root as I know the problems. Thanks for suggesting. I needed to change the methanol.itp and methanol216.gro which could be possible only through root. <br ><br >regards<br ><br >sharada <br ><br ></TD>
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