[gmx-users] Renaming of the chains in time of simulation (like ABC...to X)
Dear GROMACS users and experts, My protein is a trimer (ABC) and I am running md : on binding of a small peptide (chain-D) to a trimer (chain ABC). The peptide binds with both A and B (that means near interface region) I am following the lysozyme tutorial to build the run. I completed the run, but when I was trying to analyze the rmsd-graph of the D-peptide only (ligand peptide), it is becoming difficult to separate the chains. Because in the vmd, when I am opening the trajectory file, I found that all the chain identifiers are converted to X. That means A,B,C and D - all four chains are renamed as X. In the topology files, i checked that all the chains and their name are proper and separate, like in files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp Therefore, my question is: when the chain-identifiers are getting converted to X? And how can I correct this? May be I am missing some very basic thing, but I can't find which one. I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much. Sincerely Nil -- 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] Renaming of the chains in time of simulation (like ABC...to X)
Hi Mark and GROMACS users, Thanks for your reply. I checked with less but there is no chain information. The file I am loading in VMD: is first *.gro and then loading *.xtc or *.trr files on it. But after loading .gro or .xtc or .trr file ; when I go to the ExtensionsAnalysisSequence Viewer of the vmd-GUI, it shows that all the chain names are X only. Therefore, I also checked that in the other .gro files which I used in time of md-preparation are also chainX (like in mymoleculename_processed.gro, the output of pdb2gmx is chainX only ). Because, I think chain informations exist only in the topology files (.top and .itp). So the difficulties I am facing is how to load the information from the .top and .itp files in vmd. Thus, I can visualize the chain sepreately (all four chains A,B,C and D) and measure each chain's RMSD change seperately by saving trajectoories for each chain. Thanks again for the reply. Please help. Thanking you Sincerely nil --- Date: Mon, 25 May 2015 18:01:11 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Renaming of the chains in time of simulation (like ABC...to X) Message-ID: CAMNuMAQtRFh0CR8m8=hcahlw1au0axay_dvnlzqurjidd7c...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Does the file you're opening in VMD have any information about the chain? You'll need to look at it, e.g. with less. Mark On Mon, May 25, 2015 at 6:44 PM Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear GROMACS users and experts, My protein is a trimer (ABC) and I am running md : on binding of a small peptide (chain-D) to a trimer (chain ABC). The peptide binds with both A and B (that means near interface region) I am following the lysozyme tutorial to build the run. I completed the run, but when I was trying to analyze the rmsd-graph of the D-peptide only (ligand peptide), it is becoming difficult to separate the chains. Because in the vmd, when I am opening the trajectory file, I found that all the chain identifiers are converted to X. That means A,B,C and D - all four chains are renamed as X. In the topology files, i checked that all the chains and their name are proper and separate, like in files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp Therefore, my question is: when the chain-identifiers are getting converted to X? And how can I correct this? May be I am missing some very basic thing, but I can't find which one. I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much. Sincerely Nil -- -- 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] gromacs.org_gmx-users Digest, Vol 125, Issue 20
Thank you very much! Sincerely nil On Thu, Sep 4, 2014 at 2:51 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. adding ions in the genion for multimeric proteins (Ambarnil Ghosh) 2. Re: adding ions in the genion for multimeric proteins (rajat desikan) 3. Re: adding ions in the genion for multimeric proteins (Dallas Warren) 4. Re: Structuring as function of z - gmx order (Dallas Warren) 5. Regarding gromacs installation (Sathya) 6. Re: Regarding gromacs installation (Chandan Choudhury) 7. Re: Regarding gromacs installation (Chandan Choudhury) -- Message: 1 Date: Thu, 4 Sep 2014 12:33:34 +0900 From: Ambarnil Ghosh ambargrom...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] adding ions in the genion for multimeric proteins Message-ID: capn+stt-mjzvwqelxshbzadebfreohjhhto11gfbrqsnqdq...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- Message: 2 Date: Thu, 4 Sep 2014 09:55:14 +0530 From: rajat desikan rajatdesi...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] adding ions in the genion for multimeric proteins Message-ID: CA+d_LwtwDuwF-akbU-kQTSX-r7B49+PkQxMW= nbyw1xnzg1...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Use genion -neutral and let gromacs do that hard work. Regards, On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Message: 3 Date: Thu, 04 Sep 2014 03:56:18 + From: Dallas Warren dallas.war...@monash.edu To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] adding ions in the genion for multimeric proteins Message-ID
