<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">Dear gmx-users,</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">I am try to simulate the protein-drug, and have used drg.itp from prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I issue a grompp command for minimization,grompp gives a fatal error.</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">The error is:</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><span style="mso-spacerun: yes"><font face="Times New Roman"> </font></span></span><span style="FONT-FAMILY: Tahoma; FONT-SIZE: 12pt" lang="EN-US"> </span><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">Error 0 [file "unk.itp",line 4] </font></span></p>
<p style="TEXT-INDENT: 12pt; MARGIN: 0cm 0cm 0pt; mso-char-indent-count: 1.0" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">Not enough parameters</font></span></p>
<p style="TEXT-INDENT: 12pt; MARGIN: 0cm 0cm 0pt; mso-char-indent-count: 1.0" class="MsoNormal"><span style="FONT-SIZE: 12pt" lang="EN-US"><font face="Times New Roman">…..</font></span></p>
<p style="TEXT-ALIGN: left; TEXT-INDENT: 12pt; MARGIN: 0cm 0cm 0pt; mso-pagination: widow-orphan; mso-char-indent-count: 1.0; tab-stops: 45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt" class="MsoNormal" align="left">
<span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">Fatal error:</font></span></p>
<p style="TEXT-INDENT: 12pt; MARGIN: 0cm 0cm 0pt; mso-char-indent-count: 1.0" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">Bonded/nonbonded atom type '1' not found!</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">My pro.top file:</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>#include “ffg43a1.itp”</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>#include “unk.itp”</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>[molecules]</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>Protein<span style="mso-spacerun: yes"> </span>1</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>UNK<span style="mso-spacerun: yes"> </span>1</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>SOL<span style="mso-spacerun: yes"> </span>109324</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">My drg.itp file:</font></span></p>
<p style="TEXT-INDENT: -12pt; MARGIN: 0cm 0cm 0pt 12pt; mso-char-indent-count: -1.0" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span></font></span><font face="Times New Roman"><span style="FONT-SIZE: 12pt" lang="EN-US">[ atoms ]<br>
; nr type resnr resid atom cgnr charge mass<br> 1 CR1 1 UNK CBF 1 0.003 12.0110 <br> 2 HC 1 UNK HBF 1 0.035 1.0080 <br> ...............<br>[ bonds ]<br>
; ai aj fu c0, c1, ...<br> 1 2 2 0.109 12300000.0 0.109 12300000.0 ; CBF HBF <br> 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CBF CBG <br> .............<br>[ pairs ]<br>; ai aj fu c0, c1, ...<br>
1 6 1 ; CBF NBK <br> 1 9 1 ; CBF CBI <br> .................<br>[ angles ]<br>; ai aj ak fu c0, c1, ...<br>
2 1 3 2 120.0 505.0 120.0 505.0 ; HBF CBF CBG <br> 2 1 13 2 120.0 505.0 120.0 505.0 ; HBF CBF CBE <br> ................<br>[ dihedrals ]<br>; ai aj ak al fu c0, c1, m, ...<br>
1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp CBF CBE CBG HBF <br> 3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBG </span><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"></span></font></p>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">Maybe someone knows what the problem might be?How can I deal with this problem? </font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-SIZE: 12pt; mso-font-kerning: 0pt" lang="EN-US"><font face="Times New Roman">Thanks for your help!</font></span></div>