On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 3/18/13 3:42 AM, Shima Arasteh wrote: > >> Thanks for all your replies. >> But I' d like to know what the meanings of S and D are? Why sometimes we >> should write DPOSRE, sometimes POSRE, and sometimes DPOSRES? >> >> > I already explained what the "D" prefix means. If this is unclear to you, > please read about cpp macros. When processing a topology, grompp works > just like cpp works on C source code. > See also http://www.gromacs.org/Documentation/Include_File_Mechanism Mark The choice between POSRE and POSRES is completely irrelevant except for > your own usage and consistency in so doing. Gromacs defaults to using > POSRES to indicate POSition REStraints. If you build some custom topology, > you can use whatever you want. it doesn't matter at all, as long as you > are consistent in invoking it. > > -Justin > > > >> >> Sincerely, >> Shima >> >> >> ______________________________**__ >> From: Shima Arasteh <shima_arasteh2...@yahoo.com> >> To: Justin Lemkul <jalem...@vt.edu>; Discussion list for GROMACS users < >> gmx-users@gromacs.org> >> Sent: Monday, March 18, 2013 10:35 AM >> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints >> >> To solve the problem, I changed all DPOSREs in if statments to POSRE. >> Again I get the fatal error. This error states that I have inserted >> topology section "position_restraints" in a wrong place. I checked again >> the itp files included in my top file. They are matched correctly! Did I >> modified the settings incorrectly? >> >> What would be other potent problems? >> >> Please help me. >> Thanks for your help. >> >> >> >> Sincerely, >> Shima >> >> >> ----- Original Message ----- >> From: Justin Lemkul <jalem...@vt.edu> >> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for >> GROMACS users <gmx-users@gromacs.org> >> Cc: >> Sent: Sunday, March 17, 2013 5:19 PM >> Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints >> >> >> >> On 3/17/13 6:50 AM, Shima Arasteh wrote: >> >>> Thanks for your replies. >>> As you suggested, I did as follows: >>> 1. made index groups of two chains of my protein >>> 2.Then applied genrestr in this command to generate 2 itp files: >>> chainA_posre.itp and chainB_posre.itp >>> #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 100000 100000 >>> 100000 -n index-chain.ndx >>> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 100000 100000 >>> 100000 -n index-chain.ndx >>> >>> 3.Next, I included the itp files as follow in my top file: >>> >>> ; Include chain topologies >>> #include "topol_Protein_chain_A.itp" >>> #ifdef DPOSRE >>> #include "chainA_posre.itp" >>> #endif >>> #include "topol_Protein_chain_B.itp" >>> #ifdef DPOSRE >>> #include "chainB_posre.itp" >>> #endif >>> >>> 4. I also added this line to my mdp file: >>> define = -DPOSRE >>> >>> 5. In addition I added these at the top of itp files for bothe >>> restrained chains: >>> #ifdef DPOSRE >>> #endif >>> >>> Now when I run the command : >>> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr >>> >>> I don't get any errors. >>> But when I run the mdrun I don't see any position restraint terms in my >>> log file. >>> Would you please let me know your suggestions in this about? Did I do >>> any steps by mistake? >>> >>> >> Yes, again there is a problem with the #ifdef statements. If you use: >> >> #ifdef DPOSRE >> ... >> #endif >> >> the corresponding "define" statement is -DDPOSRE. Think of the first "D" >> in the >> "define" statement as "I am defining the following string to be true." >> Your >> .mdp file corresponds to the use of: >> >> #ifdef POSRE >> ... >> #endif >> >> -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 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> > -- 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