[gmx-users] DSSP
Hello, Thank you all for your help! I got it working by downloading the executables directly and setting the path but i do get the Program do_dssp, VERSION 5.0 Source code file: /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c, line: 670 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. error. No matter which version i specify, it persists, any ideas? Cheers, Nicholas -- 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] DSSP
Yes, this is the command i am using: do_dssp -s npt-nopr.tpr -f npt-nopr.trr -o fws-ss.xpm -ver 2 whether i include -ver 2 or not makes no difference, I still get the same error. Cheers, Nicholas On 25 August 2014 15:53, Mark Abraham mark.j.abra...@gmail.com wrote: Have you read and followed gmx do_dssp -h? Mark On Mon, Aug 25, 2014 at 2:21 PM, Nikolaos Michelarakis nm...@york.ac.uk wrote: Hello, Thank you all for your help! I got it working by downloading the executables directly and setting the path but i do get the Program do_dssp, VERSION 5.0 Source code file: /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxana/gmx_do_dssp.c, line: 670 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. error. No matter which version i specify, it persists, any ideas? Cheers, Nicholas -- 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.
[gmx-users] DSSP
Hello, I am trying to do a secondary structure analysis to get the percentages of each secondary structure in my protein. I know i can use do_dssp but unfortunately DSSP is not installed on the cluster that i have been using and i do not have the acess to install it. Any other ways to do it? or would anyone be able to run it for me? I need it for 3 structures, for 3 different forcefields, 9 structures overall. Thanks a lot, Nicholas -- 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] DSSP
Hi, Thank you for your answer, could you please give me some more info on where to find them and how to use them for the whole trajectory? Cheers, Nicholas -- 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.
[gmx-users] Measuring distances between residues and visualising the results
Hello, I am trying to measure the distances between certain residues over the course of my simulation. I have created an index with these residues. So far i have tried using gmx mdmat but since there are only five residues the resulting map consists of 25 large boxes, of different shades, which is not very useful. I have also tried using gmx distance but I am not sure if I am using it correctly. When it prompts me to select the groups do I choose the index group twice? Any suggestions on how to better visualize the gmx_mdmat results or use gmx distance accurately? Thanks a lot, Nicholas -- 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] Solvent error?
These are the commands i used: pdb2gmx -ignh -f 3ZK3-etc.pdb -o fws.gro -p fws.top for the topology and selected my custom AMBER forcefield which i had placed in the working directory and chose tip3 water editconf -f fws.gro -o fws-PBC.gro -bt dodecahedron -d 1.2 for the box gmx solvate -cp fws-PBC.gro -cs spc216.gro -o solv.gro -p fws.top for the solvation grompp -f em-sol-pme.mdp -c fws-b4ion.gro -p fws.top -o ion.tpr when i try to add the ions i get the error. Cheers! Nicholas -- 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] Solvent error?
Sorry, I just have all the commands saved and just copy, paste and customise according to the files i am using. I used: grompp -f em-sol-pme.mdp -c solv.gro -p fws.top -o ion.tpr not fws-b4ion.gro Thanks, Nick -- 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] Solvent error? (Mark Abraham)
I added them manually in the initial fws.gro file and changed the number on top. If you see the solv.gro file, they are included, along with the solvent, but for some reason, 42 less solvent atoms are added. Thanks, Nicholas -- 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.
[gmx-users] Solvent error?
Hello again, I am trying to include a ligand in my structure, which consists of 42 atoms, using an .itp file, in the AMBER forcefield. The itp was generated by antechamber and is the ligand_backup.itp. Everything works fine until I try to solvate it. It seems that the gro file produced by the solvation includes 42 less atoms, therefore i get the following error when i try to run the energy minimization. Program gmx, VERSION 5.0 Source code file: /home/jslatter/programs/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/grompp.c, line: 603 Fatal error: number of coordinates in coordinate file (solv.gro, 57310) does not match topology (fws.top, 57352) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Are the 42 atoms of the ligand not included in the solv.gro file? As usual, all the files that i have used are in the link: https://drive.google.com/folderview?id=0Bxa-J2wEpEeqOWFsOUUyNDVPYWcusp=sharing Cheers, Nicholas -- 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.
[gmx-users] Iron containing structure simulation crash
Hello again, I finally managed to introduce the iron into my structure and generate a topology. However, when i first run the initial energy minimization, either in vacuum or with solvent, i get the following message: It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often notneeded for preparing to run molecular dynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 500. Potential Energy = -4.2946888e+05 Maximum force = 6.7161971e+08 on atom 2832 Norm of force = 1.7847602e+07 however, a .gro file is produced. When I try to run the next step with this .gro file I get a bunch of LINCS warnings and after a few steps the simulation crashes with this message: /opt/gridengine/default/spool/compute-0-5/job_scripts/11107: line 15: 5738 Segmentation fault (core dumped) mdrun -v -nt 12 -deffnm nvt-pr I also get a bunch of .pdb files named accordingly to each step. Could anyone explain to me what is going wrong? I can provide links to all files if required. Thanks again, Nicholas -- 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] Iron containing structure simulation crash
An output coordinate file is always produced unless mdrun completely fails and seg faults. That doesn't mean the coordinates are sane. It's meant to help you diagnose in cases like this where you have an absurd force on some atom. What is atom 2832? What's around it? Is there anything obviously clashing with it? Also check the topology for errors. -Justin The atom is the iron that I introduced. It is bound to an oxygen which is itself bound to the carbon of a ring. It is found on the spot where the ligand, not introduced in the simulation yet, is binding to the protein. There are a few carbons and nitrogens but nothing in close proximity or clashing with it. The topology seems ok to me. This is the link to the file, the iron shows a charge of +3, could this be the cause of such a great force? https://drive.google.com/file/d/0Bxa-J2wEpEeqTC1UX2tNOG1LVms/edit?usp=sharing Thank you again, Nicholas -- 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 124, Issue 58
Thank you very much for your answer! this is the link to the whole forcefield directory: https://drive.google.com/folderview?id=0Bxa-J2wEpEeqbnZDVmpmQ0JGcUEusp=sharing Since it's my first time doing something like that, i might have done something wrong in adding the iron in the forcefield. Since iron was already present in the heme group of the forcefield i used FE3+ as a name. please let me know if I have done something wrong. I tried playing around with the charge of the iron, changed it to 0.4, and these are the new files i got for every step, along with the topology. This time the force on the whole structure was larger and a lot smaller on the oxygen bound on the iron: https://drive.google.com/folderview?id=0Bxa-J2wEpEeqME82TjhJUnQ0TzQusp=sharing I would appreciate it If you could take a look at the forcefield and let me know if everything is correct in there and I will try finding the correct parameters. Thank you again for all your help. Nicholas On 12 August 2014 18:35, 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. Setting Non-bonded Scaling Constant for Amber FF (Johnny Lu) 2. Re: Setting Non-bonded Scaling Constant for Amber FF (Justin Lemkul) 3. Re: Iron containing structure simulation crash (Nikolaos Michelarakis) 4. Re: Iron containing structure simulation crash (Nikolaos Michelarakis) 5. Re: Iron containing structure simulation crash (Justin Lemkul) 6. Re: potential energy (Meenakshi Rajput) 7. Re: Polymer not diffusing into membrane (Alex s) -- Message: 1 Date: Tue, 12 Aug 2014 11:57:45 -0400 From: Johnny Lu johnny.lu...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Setting Non-bonded Scaling Constant for Amber FF Message-ID: CACFK4+NF-YOP3tJ6TZZKm9zJhRob1Wv-87ZB= nf50rqnq5b...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi. I'm a first year PhD student, and wonder if we have to set the equivalent of scnb and scee (1-4 nonbond scaling facor for vdw and for electrostatic) in the gromacs mdp file when we use the Amber99SB force field in gromacs? Thank you in advance. -- Message: 2 Date: Tue, 12 Aug 2014 12:00:04 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Setting Non-bonded Scaling Constant for Amber FF Message-ID: 53ea3a04.1040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 8/12/14, 11:57 AM, Johnny Lu wrote: Hi. I'm a first year PhD student, and wonder if we have to set the equivalent of scnb and scee (1-4 nonbond scaling facor for vdw and for electrostatic) in the gromacs mdp file when we use the Amber99SB force field in gromacs? You don't. These values are specified in the [defaults] directive in forcefield.itp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Message: 3 Date: Tue, 12 Aug 2014 17:20:31 +0100 From: Nikolaos Michelarakis nm...@york.ac.uk To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Iron containing structure simulation crash Message-ID: CADp34cnycCQxS7gbU3WzL5Jf8L7aRhj= edgr5xqg591dco3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 An output coordinate file is always produced unless mdrun completely fails and seg faults. That doesn't mean the coordinates are sane. It's meant to help you diagnose in cases like this where you have an absurd force on some atom. What is atom 2832? What's around it? Is there anything obviously clashing with it? Also check the topology for errors. -Justin The atom is the iron that I introduced. It is bound to an oxygen which is itself bound to the carbon of a ring. It is found on the spot where the ligand, not introduced in the simulation yet, is binding to the protein. There are a few carbons
Re: [gmx-users] Protein simulation including ligand with Fe(III)
Hello again, Since I could not find any reliable parameters for the Fe-O for the GROMOS 96 forcefield I decided to modify it to use the parameters for its Fe-N in its HEME group. While reading through the gromos54a7 files i saw that it has parameters for the Fe-O bond so I thought that it might be able to deal with my molecule. I run pdb2gmx on my molecule, which included the protein and the iron, and a topology was produced, giving no errors. However, when I opened the topology, there is no Fe present in it. Sorry if that's a silly question but shouldn't it be in there? I can include the files if required. Thanks again. Nicholas -- 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] Protein simulation including ligand with Fe(III)
Hi Justin, Thank you for your answer. I was going to use the parameters from an MM paper but since you mentioned that, any idea where I can find some better parameters? I don't want them to be perfect and I don't have time for QM, just something so the protein won't blow up up. Thanks, Nicholas -- 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.
[gmx-users] Licam Fe parameters
Hello All, I am trying to simulate a structure containing a licam-4 or licam-5 ligand with an iron (Fe) bound on it. I was wondering if anyone has any parameters for this iron? Thank you very much in advance! Cheers, Nicholas -- 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] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters
Hello again, This what I have been trying to do so far. This is the command to run the script: ./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff and this is the error I have been getting along with 2 Notes: NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in charmm36-mar2014.ff/forcefield.doc : 2b8 NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top 96 142 The file names I am using are: 2e7z-ptc.str charmm36-mar2014.ff 2e7z-ptc.mol2 cgenff_charmm2gmx.py These are the contents of the .mol2 and .str files respectively: https://drive.google.com/file/d/0BzqRbRx4Ynf0TUg3blBOTmV0Qzg/edit?usp=sharing (mol2) https://drive.google.com/file/d/0BzqRbRx4Ynf0VThMSnNYMU1XVmM/edit?usp=sharing (str) Thanks a lot, Nicholas -- 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] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters
Dear Justin, Thank you very much for your reply. I have tried the converter but I think I don't have enough experience to get the CHARMM files working properly with the converter. If I sent you the files, would it be possible to do it for me or guide me through it? Thanks again, Nicholas On 23 June 2014 17:42, Justin Lemkul jalem...@vt.edu wrote: On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote: Dear All, First, I would like to say that I have started using GROMACS during this last month so please take that in mind when answering. I am trying to run an MD simulation of an enzyme which contains some non standard residues such as a tungsten metal ion and some other cofactors. I understand that I need to create the topology and find the parameters for these non-standard residues. Reading the manual I saw about .itp files and, correct me if I'm wrong, but it's my understanding that these are used for parts of the topology which are not bonded or intergrated in the structure that is being simulated. My question is how do I include these bonded parts in the simulation? An .itp file specifies a distinct [moleculetype] that shares no bonded interactions with any other species in the system. The development version of the code has the capability to do intermolecular bondeds, but at present the distinction is true enough. Are you asking how to include actual bonds between your non-standard residues and other parts of the system? If so, then the only options are: 1. Create an .rtp entry for your non-standard residue(s) and modify specbond.dat accordingly, as these will likely be non-linear bonds. That way, you'll have a single [moleculetype] in which you will have bonds between the different residues. 2. Use git to obtain the developmental version of the code that has intermolecular bond capabilities. I don't recall offhand which patch has it or if it's even been merged, but it's in the Gerrit repo, at least. My second question, someone has already developed a topology and some parameters for this structure but in CHARM. I tried using one of the two scripts available online to convert them to GROMACS but to no avail. Is there a way to automatically do this or will I have to go all over it by hand? If you have a stream file, we have a converter: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs It was designed to interface with CGenFF .str files from ParamChem, but it should do the job. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
