Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul 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 >> To: Justin Lemkul ; 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 >> To: Shima Arasteh ; Discussion list for >> GROMACS users >> 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 10 10 >>> 10 -n index-chain.ndx >>> #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 >>> 10 -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 listgmx-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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
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. 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 To: Justin Lemkul ; Discussion list for GROMACS users 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 To: Shima Arasteh ; Discussion list for GROMACS users 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 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/18/13 3:05 AM, Shima Arasteh wrote: 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? Clearly. Fatal errors mean something is very wrong. In principle, what you showed before was correct. If that wasn't an actual topology snippet or you've done something else wrong, then I haven't seen what it is. -Justin What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users 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 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
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 To: Justin Lemkul ; Discussion list for GROMACS users 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 To: Shima Arasteh ; Discussion list for GROMACS users 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 10 10 > 10 -n index-chain.ndx > #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 > 10 -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 listgmx-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
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 To: Shima Arasteh ; Discussion list for GROMACS users 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 10 10 > 10 -n index-chain.ndx > #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 > 10 -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 listgmx-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
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 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
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 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -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? Thanks in advance. Sincerely, Shima From: Justin Lemkul To: Discussion list for GROMACS users Sent: Saturday, March 16, 2013 4:06 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/16/13 8:34 AM, Shima Arasteh wrote: > Thanks. > As I understood from your emails, I need to make index groups of separate > chains of my protein, use the index file in order to use in genrestr command > and then include the specific itp files for each groups in top file? > Do you mean this? Am I right? > Yes. Try it. > One more thing that I need to know is that how it is possible to make an > index group except the options appear after running make index command? > Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage. It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc. -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 8:34 AM, Shima Arasteh wrote: Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? Yes. Try it. One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage. It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc. -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 3:39 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/16/13 7:09 AM, Shima Arasteh wrote: > Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? > It would not be possible because I don't see any option for seperate chains > when running genrestr command. > You need to provide a sensible index group to genrestr to create such groups. -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 7:09 AM, Shima Arasteh wrote: Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. You need to provide a sensible index group to genrestr to create such groups. -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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. Thanks in advance. Sincerely, Shima From: Mark Abraham To: Shima Arasteh ; Discussion list for GROMACS users Sent: Saturday, March 16, 2013 2:21 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh wrote: As you said I changed define in mdp file to define=-DPOSRE . > >I also included backbone.itp file as this: > > >; Include chain topologies >#include "topol_Protein_chain_A.itp" >#ifdef POSRE >#include "backbone_posre.itp" > >#endif >#include "topol_Protein_chain_B.itp" >#ifdef POSRE >#include "backbone_posre.itp" >#endif > > > ; Include POPC chain topology >#include "popc.itp" > >; Include water topology >#include "./charmm36-modified.ff/tip3p.itp" > >#ifdef POSRES_WATER >; Position restraint for each water oxygen >[ position_restraints ] >; i funct fcx fcy fcz > 1 1 1000 1000 1000 >#endif > > > >; Include topology for ions >#include "./charmm36-modified.ff/ions.itp" > >[ system ] >; Name >Protein > >[ molecules ] >; Compound #mols >Protein_chain_A 1 >Protein_chain_B 1 >POPC 238 >SOL 19936 >CL 2 > >But I get this fatal error that my include part for position restraints is not >correct: >Fatal error: >[ file backbone_posre.itp, line 79 ]: >Atom index (364) in position_restraints out of bounds (1-360). >This probably means that you have inserted topology section >"position_restraints" >in a part belonging to a different molecule than you intended to. >In that case move the "position_restraints" section to the right molecule. >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors > >Would you please give me suggestions? > The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark >Thanks in advance. > >Sincerely, >Shima > > >- Original Message - >From: Justin Lemkul >To: Shima Arasteh ; Discussion list for GROMACS >users >Cc: >Sent: Saturday, March 16, 2013 12:25 AM >Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints > > > >On 3/15/13 9:43 AM, Shima Arasteh wrote: >> I also included the position restraints as follows in my top file: >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #ifdef POSRE >> #include "backbone_posre.itp" >> #include "strong_posre.itp" >> #endif >> #include "topol_Protein_chain_B.itp" >> #ifdef POSRE >> #include "strong_posre.itp" >> #include "backbone_posre.itp" >> #endif >> >> As I described earlier, I included position restraints of backbone in top >> file and also added define = -DPOSRES to minim.mdp file. But it seems that >> the position restrains have not been included. Would you please suggest me >> how I can apply position restraints effectively? >> > >It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your >topology, what you need is -DPOSRE. It is very easy to tell when position >restraints are being applied. A position restraint energy term is written to >the .log and .edr files. If it's not there, you're not applying restraints. > >-Justin > >> Thanks in advance. >> Your suggestions would be appreciated. >> Shima >> >> >> -- Forwarded message -- >> From: Shima Arasteh >> Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) >> Subject: Fw: Fwd: [gmx-users] position restraints >> To: Discussion list for GROMACS users >> >> Dear users, >> >> >> Although I put the position restraints on backbone, I get RMSD around >> 0.2 nm. Is it usual? >> This deviation is just for a minimization step only. I' m on doubt >> about keeping the backbone in a fix secondary structure. >> I' d prefer to restraint the backbone completely. Is it possible? >> >> Thanks in advance. >> >> >> >> Restraints allow, by definition, for slight deviations. >> >> Erik >> * Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh wrote: > As you said I changed define in mdp file to define=-DPOSRE . > > I also included backbone.itp file as this: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #endif > > > ; Include POPC chain topology > #include "popc.itp" > > ; Include water topology > #include "./charmm36-modified.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > > > ; Include topology for ions > #include "./charmm36-modified.ff/ions.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound#mols > Protein_chain_A 1 > Protein_chain_B 1 > POPC238 > SOL19936 > CL2 > > But I get this fatal error that my include part for position restraints is > not correct: > Fatal error: > [ file backbone_posre.itp, line 79 ]: > Atom index (364) in position_restraints out of bounds (1-360). > This probably means that you have inserted topology section > "position_restraints" > in a part belonging to a different molecule than you intended to. > In that case move the "position_restraints" section to the right molecule. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Would you please give me suggestions? > The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark > > Thanks in advance. > > Sincerely, > Shima > > - Original Message - > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for > GROMACS users > Cc: > Sent: Saturday, March 16, 2013 12:25 AM > Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints > > > > On 3/15/13 9:43 AM, Shima Arasteh wrote: > > I also included the position restraints as follows in my top file: > > > > ; Include chain topologies > > #include "topol_Protein_chain_A.itp" > > #ifdef POSRE > > #include "backbone_posre.itp" > > #include "strong_posre.itp" > > #endif > > #include "topol_Protein_chain_B.itp" > > #ifdef POSRE > > #include "strong_posre.itp" > > #include "backbone_posre.itp" > > #endif > > > > As I described earlier, I included position restraints of backbone in > top file and also added define = -DPOSRES to minim.mdp file. But it seems > that the position restrains have not been included. Would you please > suggest me how I can apply position restraints effectively? > > > > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your > topology, what you need is -DPOSRE. It is very easy to tell when position > restraints are being applied. A position restraint energy term is written > to > the .log and .edr files. If it's not there, you're not applying > restraints. > > -Justin > > > Thanks in advance. > > Your suggestions would be appreciated. > > Shima > > > > > > -- Forwarded message -- > > From: Shima Arasteh > > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > > Subject: Fw: Fwd: [gmx-users] position restraints > > To: Discussion list for GROMACS users > > > > Dear users, > > > > > > Although I put the position restraints on backbone, I get RMSD around > > 0.2 nm. Is it usual? > > This deviation is just for a minimization step only. I' m on doubt > > about keeping the backbone in a fix secondary structure. > > I' d prefer to restraint the backbone completely. Is it possible? > > > > Thanks in advance. > > > > > > > > Restraints allow, by definition, for slight deviations. > > > > Erik > > * Please don't post (un)subscribe requests to the list. Use thewww > > interface or send it to gmx-users-requ...@gromacs.org. > > > > > > > > > > Dear gmx users, > > > > I want to use restraints on backbone of my protein to keep its secondary > > structure during minimization and equilibration steps. To do so, I > > generated backbone-restrain.itp and then included it to top file. Next, > &g
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "backbone_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "./charmm36-modified.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-modified.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: > I also included the position restraints as follows in my top file: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #include "strong_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "strong_posre.itp" > #include "backbone_posre.itp" > #endif > > As I described earlier, I included position restraints of backbone in top > file and also added define = -DPOSRES to minim.mdp file. But it seems that > the position restrains have not been included. Would you please suggest me > how I can apply position restraints effectively? > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin > Thanks in advance. > Your suggestions would be appreciated. > Shima > > > -- Forwarded message -- > From: Shima Arasteh > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > Subject: Fw: Fwd: [gmx-users] position restraints > To: Discussion list for GROMACS users > > Dear users, > > > Although I put the position restraints on backbone, I get RMSD around > 0.2 nm. Is it usual? > This deviation is just for a minimization step only. I' m on doubt > about keeping the backbone in a fix secondary structure. > I' d prefer to restraint the backbone completely. Is it possible? > > Thanks in advance. > > > > Restraints allow, by definition, for slight deviations. > > Erik > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > > > > Dear gmx users, > > I want to use restraints on backbone of my protein to keep its secondary > structure during minimization and equilibration steps. To do so, I > generated backbone-restrain.itp and then included it to top file. Next, > added define = -DPOSRES to minim.mdp file. > After minimization, when I check the minimization output file, I saw > that the backbone of input and output files are not exactly the same. > Is there any step which I have not done to set the restraints correctly? > > > Thanks in advance. > > Sincerely, > Shima > -- 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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "backbone_posre.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "./charmm36-modified.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "./charmm36-modified.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: > I also included the position restraints as follows in my top file: > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRE > #include "backbone_posre.itp" > #include "strong_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRE > #include "strong_posre.itp" > #include "backbone_posre.itp" > #endif > > As I described earlier, I included position restraints of backbone in top > file and also added define = -DPOSRES to minim.mdp file. But it seems that > the position restrains have not been included. Would you please suggest me > how I can apply position restraints effectively? > It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin > Thanks in advance. > Your suggestions would be appreciated. > Shima > > > -- Forwarded message -- > From: Shima Arasteh > Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) > Subject: Fw: Fwd: [gmx-users] position restraints > To: Discussion list for GROMACS users > > Dear users, > > > Although I put the position restraints on backbone, I get RMSD around > 0.2 nm. Is it usual? > This deviation is just for a minimization step only. I' m on doubt > about keeping the backbone in a fix secondary structure. > I' d prefer to restraint the backbone completely. Is it possible? > > Thanks in advance. > > > > Restraints allow, by definition, for slight deviations. > > Erik > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > > > > Dear gmx users, > > I want to use restraints on backbone of my protein to keep its secondary > structure during minimization and equilibration steps. To do so, I > generated backbone-restrain.itp and then included it to top file. Next, > added define = -DPOSRES to minim.mdp file. > After minimization, when I check the minimization output file, I saw > that the backbone of input and output files are not exactly the same. > Is there any step which I have not done to set the restraints correctly? > > > Thanks in advance. > > Sincerely, > Shima > -- 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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #include "strong_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "strong_posre.itp" #include "backbone_posre.itp" #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- 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 listgmx-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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
I also included the position restraints as follows in my top file: ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRE #include "backbone_posre.itp" #include "strong_posre.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRE #include "strong_posre.itp" #include "backbone_posre.itp" #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- 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 listgmx-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
