Dear Mark:<br><br><span style="color: rgb(102, 0, 204);">This error is being provoked at the top of the .rtp file when a line with</span><br style="color: rgb(102, 0, 204);"><span style="color: rgb(102, 0, 204);"> something like "[header]" is not parsing suitably. A while ago I suggested</span><br style="color: rgb(102, 0, 204);">
<span style="color: rgb(102, 0, 204);"> using diff on the .rtp file. Do that.</span><br style="color: rgb(102, 0, 204);"><br><br>Would you mind telling me how to do that in detail?<br><br>I tried the following and it doesn't work.<br>
<br>diff<br>[ PDM ]<br>
; designation arbitrary, C1 and C2 is -CH3<br>
<div class="im"> [ atoms ]<br>
SI1 SI 0.300 1<br>
C1 opls_069 0.000 1<br>
C2 opls_069 0.000 1<br>
O1 opls_108 -0.300 1<br>
<br>
[ bonds ]<br>
SI1 -O1<br>
SI1 C1<br>
SI1 C2<br>
SI1 O1<br>
O1 +SI1<br>
<br>
<br>
; Terminal PDMS residue ("beginning" of chain)<br>
</div>; designation arbitrary, C1 C2 and C3 is -CH3<br>
<div class="im">[ PDMB ]<br>
[ atoms ]<br>
C1 opls_069 0.000 1<br>
SI1 SI 0.300 1<br>
C2 opls_069 0.000 1<br>
C3 opls_069 0.000 1<br>
O1 opls_108 -0.300 1<br>
<br>
[ bonds ]<br>
SI1 C1<br>
SI1 C2<br>
SI1 C3<br>
SI1 O1<br>
O1 +SI1<br>
<br>
<br>
</div>; Terminal PE residue ("end" of chain)<br>
; designation arbitrary, C1 C2 and C3 is -CH3<br>
<br>
[ PDME ]<br>
[ atoms ]<br>
SI1 SI 0.000 1<br>
C1 opls_069 0.000 1<br>
C2 opls_069 0.000 1<br>
C3 opls_069 0.000 1<br>
<br>
[ bonds ]<br>
SI1 -O1<br>
SI1 C1<br>
SI1 C2<br>
SI1 C3<br>
diff<br><br><br><br>Thanks a lot in advance!<br><br><br>On Mon, May 4, 2009 at 10:15 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> Justin A. Lemkul wrote:<br>
>><br>>> Then it seems clear to me that your installation of Gromacs is faulty.<br>>> Have you tried running the test set (available on the wiki site)? If you<br>>> can describe your computer system (OS, version, compilers used,<br>
>> configuration options, etc.) then perhaps someone on the list can spot a<br>>> potential pitfall.<br>>><br>>> -Justin<br>>><br>>> Yanmei Song wrote:<br>>>><br>>>> Dear Justin:<br>
>>><br>>>> Thank you so much for your help earlier. I updated my GROMACS to<br>>>> 4.0.4. When I run pdb2gmx using the following two files. I still got<br>>>> the similar error message:<br>
>>><br>>>> Opening library file ffoplsaa.rtp<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<br>
>>> WARNING: masses will be determined based on residue and atom names,<br>>>> this can deviate from the real mass of the atom type<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat<br>
>>> Entries in atommass.dat: 178<br>>>> WARNING: vdwradii will be determined based on residue and atom names,<br>>>> this can deviate from the real mass of the atom type<br>>>> Opening library file<br>
>>> /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat<br>>>> Entries in vdwradii.dat: 28<br>>>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat<br>>>> Entries in dgsolv.dat: 7<br>
>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat<br>>>> Entries in electroneg.dat: 71<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/elements.dat<br>
>>> Entries in elements.dat: 218<br>>>> Reading pdms2.pdb...<br>>>> Read 13 atoms<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat<br>>>> 26 out of 26 lines of xlateat.dat converted succesfully<br>
>>> Analyzing pdb file<br>>>> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms<br>>>><br>>>> chain #res #atoms<br>>>> 1 ' ' 3 13<br>>>><br>
>>> All occupancies are one<br>>>> Opening library file<br>>>> /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp<br>>>> Atomtype 1<br>>>> Reading residue database... (ffoplsaa)<br>
>>> Opening library file ffoplsaa.rtp<br>>>><br>>>> -------------------------------------------------------<br>>>> Program pdb2gmx_d, VERSION 4.0.4<br>>>> Source code file: resall.c, line: 279<br>
>>><br>>>> Fatal error:<br>>>> in .rtp file at line:<br>>>><br>>>><br>>>> -------------------------------------------------------<br>><br>> This error is being provoked at the top of the .rtp file when a line with<br>
> something like "[header]" is not parsing suitably. A while ago I suggested<br>> using diff on the .rtp file. Do that.<br>><br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br><br><br><br>-- <br>Yanmei Song<br>Department of Chemical Engineering<br>ASU<br><br>