Re: [gmx-users] Making index file
Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Making index file
Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Making index file
Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom. r 14 a CA chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Making index file
Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com wrote: Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom. r 14 a CA chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Making index file
But is it necessary to renumber the residues .. Can this be done in some other way On Wed, Nov 5, 2014 at 2:49 PM, Eric Smoll ericsm...@gmail.com wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (ericsm...@gmail.com) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DE9EnrGnFrM8VW1GJ8mZGxpbmcm1Z0OplUdfj9XjGPdGqU8a%252F570IPq%252BAkNHtIKRukk6ocJHWPiA7xqADmsV8TUZlZbrIkSR%252BK6gBYiEMND8ZA%252Fo%252BNJcq%252FyHnyimSjeY%252BPfnjhz2JLHI%253D%26key%3Dc15tC0ShNvPAlOoIApu2Dqp9oX4G1Rz8cfNqvpo6GQY%253Dtc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com wrote: Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom. r 14 a CA chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Best Regards* Bharat -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Making index file
Hi, If you are going to work with multiple chains, create a .tpr with a pdb file of your system that specifies the protein chains for analysis. Here is how I would do it. Take the initial .gro configuration of your MD run, convert it into pdb using editconf. Assign chain identifiers to the protein section and create an analysis.tpr using the same .top and .mdp as before. Use this .tpr to analyse your runs. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: But is it necessary to renumber the residues .. Can this be done in some other way On Wed, Nov 5, 2014 at 2:49 PM, Eric Smoll ericsm...@gmail.com javascript:; wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (ericsm...@gmail.com javascript:;) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DE9EnrGnFrM8VW1GJ8mZGxpbmcm1Z0OplUdfj9XjGPdGqU8a%252F570IPq%252BAkNHtIKRukk6ocJHWPiA7xqADmsV8TUZlZbrIkSR%252BK6gBYiEMND8ZA%252Fo%252BNJcq%252FyHnyimSjeY%252BPfnjhz2JLHI%253D%26key%3Dc15tC0ShNvPAlOoIApu2Dqp9oX4G1Rz8cfNqvpo6GQY%253Dtc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com javascript:; wrote: Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom. r 14 a CA chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com javascript:; wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com javascript:; wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:; javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
