Hi,<br>I did the same and the simulations work properly! I think it's a matter of labels.<br><br>Esteban<br>UNSL<br>Argentina<br>--<br><br><div class="gmail_quote">2010/4/30 Saikat Banerjee <span dir="ltr"><<a href="mailto:banskt.saikat@gmail.com">banskt.saikat@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>I presume that there is a bug in gromacs-4.0.5. <br><br>When tried to run simulations with DMSO molecules there was an error report, which said:<br>
<br>"Fatal error:<br>Atomtype SD not found"<br><br>I checked extensively for the problem, and found that there is a small error in the dmso.itp file present in $GROMACS_INSTALL_DIR/share/gromacs/top/<br>
<br>Line 5 - 10 in dmso.itp file reads,<br><br>[ atoms ]<br>; nr type resnr residu atom cgnr charge<br> 1 SD 1 DMSO SD 1 0.139<br> 2 CD 1 DMSO CD1 1 0.16<br>
3 OD 1 DMSO OD 1 -0.459<br> 4 CD 1 DMSO CD2 1 0.16<br><br>I needed to change that to -<br><br>[ atoms ]<br>; nr type resnr residu atom cgnr charge mass<br>
1 SDmso 1 DMSO SD 1 0.139 32.06000<br> 2 CDmso 1 DMSO CD1 1 0.16 15.03500<br> 3 ODmso 1 DMSO OD 1 -0.459 15.99940<br> 4 CDmso 1 DMSO CD2 1 0.16 15.03500<br>
<br>Please note that the name of the type needed to be changed.<br><br>I am not sure if I was doing something wrong, or something was erroneous in GROMACS. However, the above changes makes it work.<br><br>I just thought I would report this issue so that users know where the problem is. I would like to request the GROMACS team to take note of it and do the needful.<br>
<br>Thanks,<br><br>Saikat B.<br><br>-- <br>-------------------------------------------------------------------<br>Saikat Banerjee<br>Integrated Ph.D student<br>Prof B. Bagchi's group<br>Room no. 210<br>Solid State and Structural Chemistry Unit (SSCU)<br>
Indian Institute of Science<br>Bangalore-560012<br> <br> Ph: +91-80-22933305 (lab)<br> +91-80-23602338 (lab)<br> +91-9980228606 (mobile)<br> <br> Alternate e-mail:<br> <a href="mailto:saikat@sscu.iisc.ernet.in" target="_blank">saikat@sscu.iisc.ernet.in</a><br>
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