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?
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 ======================================== -- 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 -- 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