Hi Justin,<br><br>You're right. The parameters in ffG53a6 are different from dmso.itp file. I'll compare the results with the new simulations.<br>By the way, do you know if ffG53a6 DMSO parameters are updated to those described in the paper you mention?<br>
<br>Thanks<br><br>Esteban<br><br>--<br><br><div class="gmail_quote">2010/4/30 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
<div class="im"><br>
<br>
Esteban Gabriel Vega Hissi wrote:<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>
I did the same and the simulations work properly! I think it's a matter of labels.<br>
</blockquote>
<br></div>
Not entirely. It is a matter of force fields, which sometimes have different atom nomenclature. The dmso.itp file assumes one is using ffgmx. If using Gromos96, the atom types, and perhaps even some of the parameters might have to be changed. There is a paper published about a very good DMSO model using Gromos96; I would suggest checking the parameters therein to be sure you're actually using a valid model, and not some Frankenforcefield :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Esteban<br>
UNSL<br>
Argentina<br>
--<br>
<br>
2010/4/30 Saikat Banerjee <<a href="mailto:banskt.saikat@gmail.com" target="_blank">banskt.saikat@gmail.com</a> <mailto:<a href="mailto:banskt.saikat@gmail.com" target="_blank">banskt.saikat@gmail.com</a>>><div>
<div></div><div class="h5"><br>
<br>
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<br>
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<br>
small error in the dmso.itp file present in<br>
$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<br>
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<br>
the problem is. I would like to request the GROMACS team to take<br>
note of it and do the needful.<br>
<br>
Thanks,<br>
<br>
Saikat B.<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>
Ph: +91-80-22933305 (lab)<br>
+91-80-23602338 (lab)<br>
+91-9980228606 (mobile)<br>
Alternate e-mail:<br></div></div>
<a href="mailto:saikat@sscu.iisc.ernet.in" target="_blank">saikat@sscu.iisc.ernet.in</a> <mailto:<a href="mailto:saikat@sscu.iisc.ernet.in" target="_blank">saikat@sscu.iisc.ernet.in</a>><br>
<a href="mailto:banskt@yahoo.co.in" target="_blank">banskt@yahoo.co.in</a> <mailto:<a href="mailto:banskt@yahoo.co.in" target="_blank">banskt@yahoo.co.in</a>><div class="im"><br>
-------------------------------------------------------------------<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br>