<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear Gramacs users,<br ><br >I am trying to simulate a peptide in Methanol. I am using Methanol216.gro file for the solvent. I could create the proper top and gro files of the peptide with the methanol solvent. However at the genbox step it says <SPAN STYLE="font-style: italic; font-weight: bold;">Number of solvent molecules =0</SPAN><br >but when I open the final .gro file it has solvent molecules. Whereas the .top file does not contain the solvent molecules. <br >I am inserting the output of genbox and .gro file for information. <br ><br ><SPAN STYLE="font-weight: bold;">genbox -cp agg2box.gro -cs methanol216.gro -o agg2_b4em.gro -p agg2.top</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Reading solute configuration</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">GROwing Monsters And Cloning Shrimps</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Containing 71 atoms in 6 residues</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Initialising van der waals distances...</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Reading solvent configuration</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">"Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001"</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">solvent configuration contains 648 atoms in 216 residues</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Initialising van der waals distances...</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Will generate new solvent configuration of 2x2x2 boxes</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Generating configuration</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Sorting configuration</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Found 1 molecule type:</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> MeOH ( 3 atoms): 1728 residues</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Calculating Overlap...</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">box_margin = 0.315</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Removed 3042 atoms that were outside the box</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Neighborsearching with a cut-off of 0.45</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Table routines are used for coulomb: FALSE</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Table routines are used for vdw: FALSE</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">System total charge: 0.000</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Neighborsearching with a cut-off of 0.45</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Grid: 14 x 15 x 13 cells</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Succesfully made neighbourlist</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">nri = 9007, nrj = 188363</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Checking Protein-Solvent overlap: tested 693 pairs, removed 63 atoms.</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Checking Solvent-Solvent overlap: tested 11134 pairs, removed 513 atoms.</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Added 522 molecules</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Generated solvent containing 1566 atoms in 522 residues</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Writing generated configuration to agg2_b4em.gro</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Back Off! I just backed up agg2_b4em.gro to ./#agg2_b4em.gro.1#</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">GROwing Monsters And Cloning Shrimps</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Output configuration contains 1637 atoms in 528 residues</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Volume : 35.0595 (nm^3)</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Density : 752.963 (g/l)</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Number of SOL molecules: 0</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Processing topology</SPAN><br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">Back Off! I just backed up agg2.top to ./#agg2.top.1#</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">-----------------------------------------------------------------------------------------------------------------------------</SPAN><br style="font-weight: bold;" >agg2_b4em.gro file reads like this......<br style="font-weight: bold;" ><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">GROwing Monsters And Cloning Shrimps</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1637</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL N 1 0.990 1.146 1.482</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL H1 2 0.961 1.053 1.507</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL H2 3 0.926 1.212 1.519</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL H3 4 0.994 1.154 1.382</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL CA 5 1.126 1.172 1.539</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL CB 6 1.229 1.061 1.497</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL CG1 7 1.372 1.085 1.552</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL CG2 8 1.189 0.918 1.542</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL C 9 1.170 1.317 1.498</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 1VAL O 10 1.202 1.344 1.382</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN N 11 1.175 1.411 1.595</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN H 12 1.145 1.386 1.687</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN CA 13 1.223 1.549 1.570</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN CB 14 1.153 1.643 1.673</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN CG 15 1.175 1.794 1.647</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN CD 16 1.115 1.887 1.752</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN OE1 17 1.180 1.929 1.847</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN NE2 18 0.990 1.924 1.740</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN HE21 19 0.936 1.892 1.662</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN HE22 20 0.949 1.985 1.808</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 2GLN C 21 1.379 1.558 1.572</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">---------</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">----------</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;">- -------</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 526MeOH Me1 1629 2.760 3.368 2.738</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 526MeOH O2 1630 2.695 3.423 2.632</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 526MeOH H3 1631 2.615 3.371 2.606</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 527MeOH Me1 1632 0.288 3.224 2.925</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 527MeOH O2 1633 0.194 3.156 2.996</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 527MeOH H3 1634 0.212 3.059 2.983</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 528MeOH Me1 1635 2.506 3.095 2.599</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 528MeOH O2 1636 2.457 3.218 2.567</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 528MeOH H3 1637 2.390 3.204 2.494</SPAN><br style="font-weight: bold;" ><SPAN STYLE="font-weight: bold;"> 3.30500 3.58500 2.95900</SPAN><br ><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 ><br >sharada<br ><br ></BODY></HTML>