<div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Hi <SPAN style="mso-spacerun: yes"> </SPAN>all users </FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>I constructed topology and gro (1.gro and 1.top) file for propane ( CH3CH2CH3) molecule from<SPAN style="mso-spacerun: yes"> </SPAN>PRODRG server as follow:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="COLOR: blue"><FONT size=3><FONT face="Times New Roman">1.go<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>PRODRG
COORDS</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>3</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>1DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAB<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>-0.128<SPAN style="mso-spacerun: yes"> </SPAN>0.172<SPAN style="mso-spacerun: yes"> </SPAN>0.000</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>1DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAA<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>-0.128<SPAN
style="mso-spacerun: yes"> </SPAN>0.019<SPAN style="mso-spacerun: yes"> </SPAN>0.000</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>1DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAC<SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>0.017<SPAN style="mso-spacerun: yes"> </SPAN>-0.033<SPAN style="mso-spacerun: yes"> </SPAN>0.000</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>0.35530<SPAN style="mso-spacerun: yes"> </SPAN>0.35530<SPAN style="mso-spacerun: yes"> </SPAN>0.35530</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="COLOR: blue"><FONT size=3><FONT face="Times New Roman">1.top<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>This file was generated by PRODRG version 061128.0522</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>PRODRG written/copyrighted by Daan van
Aalten</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>and Alexander Schuettelkopf</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>; <SPAN style="mso-spacerun: yes"> </SPAN>Questions/comments to dava@davapc1.bioch.dundee.ac.uk</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun:
yes"> </SPAN>When using this software in a publication, cite:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>A. W. Schuettelkopf and D. M. F. van Aalten (2004).<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>PRODRG - a tool for high-throughput crystallography</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>of protein-ligand complexes.</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun:
yes"> </SPAN>Acta Crystallogr. D60, 1355--1363.</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>[ moleculetype ]</FONT></div> <div class=MsoNormal dir=rtl style="MARGIN: 0cm 0cm 0pt; DIRECTION: rtl; unicode-bidi: embed; TEXT-ALIGN: left" align=right><SPAN dir=ltr><FONT face="Times New Roman" size=3>; Name nrexcl</FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times
New Roman" size=3>DRG<SPAN style="mso-spacerun: yes"> </SPAN>3</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>[ atoms ]</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>;<SPAN style="mso-spacerun: yes"> </SPAN>nr<SPAN style="mso-spacerun: yes"> </SPAN>type<SPAN style="mso-spacerun: yes"> </SPAN>resnr resid<SPAN style="mso-spacerun: yes"> </SPAN>atom<SPAN style="mso-spacerun: yes"> </SPAN>cgnr<SPAN style="mso-spacerun: yes"> </SPAN>charge<SPAN style="mso-spacerun: yes"> </SPAN>mass</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun:
yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>CH3<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAB<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>-0.012<SPAN style="mso-spacerun: yes"> </SPAN>15.0350<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>CH2<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAA<SPAN
style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.024<SPAN style="mso-spacerun: yes"> </SPAN>14.0270<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>CH3<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>DRG<SPAN style="mso-spacerun: yes"> </SPAN>CAC<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>-0.012<SPAN style="mso-spacerun: yes"> </SPAN>15.0350<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times
New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>[ bonds ]</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>; ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>fu<SPAN style="mso-spacerun: yes"> </SPAN>c0, c1, ...</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.153<SPAN style="mso-spacerun: yes"> </SPAN>334720.0<SPAN style="mso-spacerun: yes"> </SPAN>0.153<SPAN style="mso-spacerun: yes"> </SPAN>334720.0 ;<SPAN style="mso-spacerun: yes">
</SPAN>CAB<SPAN style="mso-spacerun: yes"> </SPAN>CAA<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>0.153<SPAN style="mso-spacerun: yes"> </SPAN>334720.0<SPAN style="mso-spacerun: yes"> </SPAN>0.153<SPAN style="mso-spacerun: yes"> </SPAN>334720.0 ;<SPAN style="mso-spacerun: yes"> </SPAN>CAA<SPAN style="mso-spacerun: yes"> </SPAN>CAC<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm
0pt"><FONT face="Times New Roman" size=3>[ pairs ]</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">; ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>fu<SPAN style="mso-spacerun: yes"> </SPAN>c0, c1, ...<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">[ angles ]<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">; ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes">
</SPAN>ak<SPAN style="mso-spacerun: yes"> </SPAN>fu<SPAN style="mso-spacerun: yes"> </SPAN>c0, c1, ...<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN lang=DE style="mso-ansi-language: DE"><SPAN style="mso-spacerun: yes"> </SPAN></SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>3<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>111.0<SPAN style="mso-spacerun: yes"> </SPAN>460.2<SPAN style="mso-spacerun: yes"> </SPAN>111.0<SPAN style="mso-spacerun: yes"> </SPAN>460.2 ;<SPAN style="mso-spacerun: yes"> </SPAN>CAB<SPAN style="mso-spacerun: yes"> </SPAN>CAA<SPAN style="mso-spacerun: yes"> </SPAN>CAC<SPAN
style="mso-spacerun: yes"> </SPAN></FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>[ dihedrals ]</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><FONT size=3><FONT face="Times New Roman">; ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>ak<SPAN style="mso-spacerun: yes"> </SPAN>al<SPAN style="mso-spacerun: yes"> </SPAN>fu<SPAN style="mso-spacerun: yes"> </SPAN>c0, c1, m, ...<o:p></o:p></FONT></FONT></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=DE style="mso-ansi-language: DE"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Then, I construct 88 molecule of propane with editconf and genbox :</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>editconf –f 1.gro -0<SPAN style="mso-spacerun: yes"> </SPAN>1.pdb –d <SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>0.3</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>genbox -cs 1.pdb -p 1.top -o 3.pdb -<?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:address w:st="on"><st1:Street w:st="on">box</st1:Street> 3</st1:address> 3 3</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman">then I chaned the<SPAN style="mso-spacerun: yes"> </SPAN>topology file<SPAN style="mso-spacerun: yes"> </SPAN>by adding the following phrase in the end of 1.top:<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></div>
<div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="mso-spacerun: yes"><FONT face="Times New Roman" size=3></FONT></SPAN> </div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>[ system ]</FONT></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>; Name </FONT><FONT face="Times New Roman" size=3>DRG</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>[ molecules ]</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>; Compound<SPAN style="mso-spacerun: yes"> </SPAN>#mols</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>DRG<SPAN style="mso-spacerun: yes">
</SPAN>88</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>When <SPAN style="mso-spacerun: yes"> </SPAN>I want to performer the following commend<SPAN style="mso-spacerun: yes"> </SPAN>:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>grompp -v -f grompp.mdp -c b4em.pdb -p 1.top –o</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>I encounter to this error :</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Program grompp, VERSION 3.3</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>Source code file: topio.c, line: 385</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Fatal error:</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Invalid order for directive moleculetype, file ""1.top"", line 17</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>The line 17 is [ moleculetype ].</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div><PRE>I request you all to give suggestion for this.</PRE><PRE><o:p> </o:p></PRE><PRE>I will be very thankful to you. </PRE><PRE><o:p> </o:p></PRE> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div> <div
class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></div><p> 
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