Dear Justin, One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I mix 53A6 and 43A1?
On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/26/12 9:12 AM, Venkat Reddy wrote: > >> Dear Justin, >> I haven't touched the *Mass column.* I have edited the charges only using >> "gedit" in linux. >> >> > Regardless, the masses I pointed out are wrong. You should still do the > test to #include the original topology and see if it works, then if it > does, figure out the source of the error in your file. > > -Justin > > >> On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul <jalem...@vt.edu> 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://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<h**ttp://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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> > -- > ==============================**========== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists