Hi, I did the same and the simulations work properly! I think it's a matter of labels.
Esteban UNSL Argentina -- 2010/4/30 Saikat Banerjee <[email protected]> > Hi, > > I presume that there is a bug in gromacs-4.0.5. > > When tried to run simulations with DMSO molecules there was an error > report, which said: > > "Fatal error: > Atomtype SD not found" > > 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/ > > Line 5 - 10 in dmso.itp file reads, > > [ atoms ] > ; nr type resnr residu atom cgnr charge > 1 SD 1 DMSO SD 1 0.139 > 2 CD 1 DMSO CD1 1 0.16 > 3 OD 1 DMSO OD 1 -0.459 > 4 CD 1 DMSO CD2 1 0.16 > > I needed to change that to - > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 SDmso 1 DMSO SD 1 0.139 32.06000 > 2 CDmso 1 DMSO CD1 1 0.16 15.03500 > 3 ODmso 1 DMSO OD 1 -0.459 15.99940 > 4 CDmso 1 DMSO CD2 1 0.16 15.03500 > > Please note that the name of the type needed to be changed. > > I am not sure if I was doing something wrong, or something was erroneous in > GROMACS. However, the above changes makes it work. > > 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. > > Thanks, > > Saikat B. > > -- > ------------------------------------------------------------------- > Saikat Banerjee > Integrated Ph.D student > Prof B. Bagchi's group > Room no. 210 > Solid State and Structural Chemistry Unit (SSCU) > Indian Institute of Science > Bangalore-560012 > > Ph: +91-80-22933305 (lab) > +91-80-23602338 (lab) > +91-9980228606 (mobile) > > Alternate e-mail: > [email protected] > [email protected] > ------------------------------------------------------------------- > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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