Dear Justin, I haven't touched the *Mass column.* I have edited the charges only using "gedit" in linux.
On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/26/12 12:58 AM, Venkat Reddy wrote: > >> Dear all, >> I am simulating a Protein-Drug complex. I am following Justin's tutorial. >> I >> have used *PRODRG *for generating topology. *Gaussian *has given me the >> ESP >> charges. I have edited the charges in the itp file using the *Gaussian*'s >> ESP charges*. *Then I am getting this strange error. >> >> *ERROR 1 [file protein.top, line 75]:* >> * atom C4 (Res ORP-1) has mass 0* >> * >> * >> * >> * >> * >> * >> *ERROR 2 [file protein.top, line 75]:* >> * atom C14 (Res ORP-1) has mass 0* >> >> > Probably there are some hidden line ending problems. Did you edit the > file with a plain text editor? > > Also note... > > 24 CH2 1 ORP C5 4 0.354 13.0190 >> *25 CH1 1 ORP C4 4 -0.024 14.0270* >> > > These masses don't make sense. CH2 should have a mass of 14.027 and CH1 > should have a mass of 13.019. I've never seen PRODRG get something like > this wrong; were you sure to carefully change the file? It seems something > has gone very wrong here. > > Compare the original topology (from PRODRG) with the one you edited. If > grompp succeeds using the PRODRG topology (stop using it after that point), > then the error arose due to something you did when editing the file. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
