Thank yo Justin for your help...I have generated the same topology using *ATB. *Now, I got the masses correctly (as pointed out by you). So, I'm afraid that is there any bug in PRODRG server?
On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/26/12 9:35 AM, Venkat Reddy wrote: > >> 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? >> >> >> > PRODRG doesn't even do a very good job of being compatible with 43A1, so > if you re-derive the charges correctly, the result is compatible with 53A6. > PRODRG basically just uses 43A1 atom types, the names of which are largely > the same in 53A6, even if the parameters are slightly different, and thus I > view PRODRG as a method to create generic Gromos96 topologies, given that > the user has to do a fair amount of work to create a usable topology anyway. > > -Justin > > On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul <[email protected]> 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 <[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://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<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> >>>>> <htt**p://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> >>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<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> >>>>> <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> >>>>> <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://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 [email protected] >>> 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 [email protected]. >>> * 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 [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
