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<TD>Dear Dr. Justin A. Lemkul<br ><br ><font size="4">Thank you for your reply. I tried adding the line 'SOL 522 ' at the end of the .top file <br >but genbox is deleting the line. <br >------------------------------------------------------------<br ></font><span class="sender"></span><font size="2" face="Arial"><SPAN STYLE="font-weight: bold; font-style: italic;">Output configuration contains 1076 atoms in 341 residues</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Volume : 24.1334 (nm^3)</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Density : 720.413 (g/l)</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Number of SOL molecules: 0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Processing topology</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Removing line #480 'SOL 522' from topology file (agg2.top)<br >-------------------------------------------------------------------------------------------<br ></SPAN></font><font size="4" face="Arial">Thankyou Dr. <SPAN CLASS="sender">Xavier Periole for indicating that the bonds and angle information does not match with the original Gromos distributed file. I am inserting methanol.itp file which came with gromacs distribution. I downloaded the methanol216.gro.gz from gromacs site. Should I change the bond values in the itp file? But it still does not solve the problem of 'SOL molecules'. Since .top file indicates </SPAN></font><font size="2" face="Arial"><font size="4">"#include "spc.itp". So if I change it to #methanol.itp" it should work.<br ></font><br ></font>-----------------------------------------------<br ><SPAN CLASS="sender">[<SPAN STYLE="font-weight: bold; font-style: italic;">root@ccmb top]# more methanol.itp</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">#ifndef _FF_GROMOS96</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">[ atomtypes ]</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">; type mass charge ptype c6 c12</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> OW 15.999 -0.82 A 2.6170e-3 2.6330e-6</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> CMET 15.035 0.29 A 8.8758e-3 17.8426e-6</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> H 1.008 0.4 A 0.0 0.0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;"> HW 1.008 0.41 A 0.0 0.0</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">#endif</SPAN><br ><br ><SPAN STYLE="font-weight: bold; font-style: italic;">[ moleculetype ]</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">; name nrexcl</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">Methanol 2</SPAN><br style="font-weight: bold; font-style: italic;" ><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">[ atoms ]</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">; nr type resnr residu atom cgnr charge mass</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">#ifdef _FF_GROMOS96</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">1 CMET 1 MeOH Me1 1 0.176 15.035</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">2 OMET 1 MeOH O2 1 -0.574 15.999</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">3 H 1 MeOH H3 1 0.398 1.008</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">#else</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">1 CMET 1 MeOH Me1 1 </SPAN></SPAN><font size="2" face="Arial"><SPAN CLASS="sender"><SPAN STYLE="font-weight: bold;">Regards <br > sharada</SPAN></SPAN></font><SPAN CLASS="sender"><SPAN STYLE="font-weight: bold; font-style: italic;"> 0.29 15.035</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">2 OMET 1 MeOH O2 1 -0.69 15.999</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">3 H 1 MeOH H3 1 0.40 1.008</SPAN><br style="font-weight: bold; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">#endif</SPAN><br ><br ><SPAN STYLE="font-weight: bold; text-decoration: underline; font-style: italic;">[ bonds ]</SPAN><br style="font-weight: bold; text-decoration: underline; font-style: italic;" ><SPAN STYLE="font-weight: bold; text-decoration: underline; font-style: italic;">; ai aj funct c0 c1</SPAN><br style="font-weight: bold; text-decoration: underline; font-style: italic;" ><SPAN STYLE="font-weight: bold; text-decoration: underline; font-style: italic;">1 2 1 0.13600 376560.</SPAN><br style="font-weight: bold; text-decoration: underline; font-style: italic;" ><SPAN STYLE="font-weight: bold; text-decoration: underline; font-style: italic;">2 3 1 0.10000 313800.</SPAN><br style="font-weight: bold; text-decoration: underline; font-style: italic;" ><br style="font-weight: bold; text-decoration: underline; font-style: italic;" ><SPAN STYLE="font-weight: bold; font-style: italic;">[ angles ]</SPAN><br >;<SPAN STYLE="font-weight: bold;"> ai aj ak funct c0 c1</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1 2 3 1 108.53 397.5<br ><br ><br ></SPAN>Regards <br >sharada <br >(CCMB)<SPAN STYLE="font-weight: bold;"><br style="font-weight: bold;" ></SPAN>-------------------------------------------------------------------------------------------------------------------------------------------------<br ></SPAN><br ><span style="font-weight: bold; font-style: italic;"></span><SPAN STYLE="font-weight: bold; font-style: italic;"><br ><strong><em>-- Original Message --</em></strong><br >From: "Justin A. Lemkul" <jalemkul@vt.edu><br >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br >Date: Mon, 10 Dec 2007 06:36:56 -0500<br >Subject: Re: [gmx-users] Methanol SOL :Number of solvent molecules = 0<br ><br >Quoting sharada <sharada@ccmb.res.in>:<br ><br >> 526MeOH Me1 1629 2.760 3.368 2.738<br >> 526MeOH O2 1630 2.695 3.423 2.632<br >> 526MeOH H3 1631 2.615 3.371 2.606<br >> 527MeOH Me1 1632 0.288 3.224 2.925<br >> 527MeOH O2 1633 0.194 3.156 2.996<br >> 527MeOH H3 1634 0.212 3.059 2.983<br >> 528MeOH Me1 1635 2.506 3.095 2.599<br >> 528MeOH O2 1636 2.457 3.218 2.567<br >> 528MeOH H3 1637 2.390 3.204 2.494<br >> 3.30500 3.58500 2.95900<br >> Why does it say there are no SOL molecules. Where exactly am I going wrong ?<br >> Kindly advice me. Thankyou for your patience.<br >> sharada<br >><br ><br >My guess would be that it is because there are no molecules named SOL in your<br >output. Gromacs uses SOL for water, and since your system lacks water, genbox<br >is accurately telling you there are no "SOL" within the output.<br ><br >Note the line above where genbox is telling you that it added 522 molecules, and<br >add this information into your .top file.<br ><br >-Justin<br ><br ><br >========================================<br ><br >Justin A. Lemkul<br >Graduate Research Assistant<br >Department of Biochemistry<br >Virginia Tech<br >Blacksburg, VA<br >jalemkul@vt.edu | (540) 231-9080<br >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<br ><br >========================================<br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<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.<br >Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br ></SPAN></TD>
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