Hi All,<br><div class="gmail_quote"><br>At this time, I am very much interested in using gromacs utilities for analysis with {.dcd, .psf} files. Especially, eg., for g_density.<br>Primarily, I use NAMD/VMD for my work.<br>
<br>I am following this link from NAMD mailing list: <br>
<br><a href="http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html" target="_blank">http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14046.html</a> <br>
<br>As suggest, by Axel, I was able to get the {.top} file. <br><br>However, when I used gromacs's "grompp" command:<br><br>$ grompp -f minim1.mdp -c BL1_only.pdb -p BL1_only.top -o BL1_only.tpr<br><br>I was returned with an error like this: <br>
<br>* * * <br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#<br>Generated 231 of the 231 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 231 of the 231 1-4 parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'molecule0'<br>Excluding 3 bonded neighbours molecule type 'molecule1'<br><br>NOTE 1 [file BL1_only.top, line 1880]:<br> System has non-zero total charge: -5.999999e+01<br>
<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.4<br>Source code file: /home/mandrake/rpm/BUILD/gromacs-4.5.4/src/kernel/grompp.c, line: 175<br><br>Fatal error:<br><span style="background-color: rgb(255, 255, 255);">The largest charge group contains 140 atoms. The maximum is 32.</span><br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<br>My system is a mixed bilayer with negative 60 charge on it. <br><br>I am searching gromacs mailing list and still looking for an answer. <br><br>Is there a way to use g_density with my set of files - {.psf, .pdb, .dcd} ?<br>
<br><br>Please suggest and help. <br><br>Thanks a lot,<br><font color="#888888">--- Lalit<span><span style="background-color: rgb(255, 255, 255);"></span></span><br></font><br>p.s.: All relevant files: BL1_only.pdb; BL1_only.psf; BL1_only.top & minim1.mdp can be downloaded from: <br>
<br><a href="http://lalitpkc.phy.uic.edu/%7Elalit/GROMACS_files" target="_blank">http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files</a><br>
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