Re: [gmx-users] How to remove H atom from residue in gro file?
Ho THANKS MANY THANKS I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much. Hagit. 2012/5/2 Mark Abraham mark.abra...@anu.edu.au On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore it because *each cystein is on a different chain*. So it adds H and therefor the disulfide bond is ruined during energy minimization. Is there any way to recreate such a disulfide bond (Please don't tell me again about -ss it works only on one chain. Moreover, the bond is existed on the pdf file.) or never ruined it at the first place? Yes, and the clue to how to combine the chains to give the mechanism a chance of working is on the page I linked last time: http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds Mark -- 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 -- 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: [gmx-users] How to remove H atom from residue in gro file?
On 5/2/12 6:55 AM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore it because *each cystein is on a different chain*. So it adds H and therefor the disulfide bond is ruined during energy minimization. Is there any way to recreate such a disulfide bond (Please don't tell me again about -ss it works only on one chain. Moreover, the bond is existed on the pdf file.) or never ruined it at the first place? Well you may need to use -ss, but since you don't want to hear about it, I won't say anything more... What you need to do is create a [moleculetype] that consists of both chains. The pdb2gmx option -chainsep will allow you to create a properly merged molecule that can form the intermolecular disulfide because the two molecules will be considered as one [moleculetype], as Gromacs requires. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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: [gmx-users] How to remove H atom from residue in gro file?
On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore it because *each cystein is on a different chain*. So it adds H and therefor the disulfide bond is ruined during energy minimization. Is there any way to recreate such a disulfide bond (Please don't tell me again about -ss it works only on one chain. Moreover, the bond is existed on the pdf file.) or never ruined it at the first place? Yes, and the clue to how to combine the chains to give the mechanism a chance of working is on the page I linked last time: http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds Mark -- 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: [gmx-users] How to remove H atom from residue in gro file?
Hi Maik, Thanks for the warning and the tip, I have already donwloaded and will read that paper today, it seems to be what I need. I have been working with MD for some 6 months now (I know that's not much), and have had the help of some knowledgeable people, but they are unavailable right now. I just do not have any formal training per se, only a crash course, and therefore do not really understand all that is going on. And this is one problem I do not even know how to begin to address. But thanks for all your help anyway. Best regards, Nelson -- Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Av. Bauhinia 400 CCS, Bl. E, sl 22 21941-590 Ilha do Fundão - Rio de Janeiro - RJ Brasil Tel: 55-21-2562-6759 Cel: 55-21-9267-3067 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to remove H atom from residue in gro file?
Dear All, In working with Nelson on his problem (below), I made some headway into figuring out what is going on with the ffG43a1p force field files. I know a few others have asked questions about it across this list, so I thought I would send this out to everyone. By modifying a few entries in the .hdb file, the problems seem to be alleviated (as in, the residues are recognized and pdb2gmx proceeds without any errors). It seems that perhaps the formatting of the .hdb file has changed since a previous version of Gromacs, but this change has not been reflected in the ffG43a1p* files. I made no changes to the parameters or the entries in the original files, only the formatting. If anyone has a need for the complete set of ffG43a1p files, please email me (off-list), and I will be happy to send them along. If there is a widespread demand for them, I will upload them to the User Contributions site. Hopefully they will work :) I have not tested them extensively, but I looked into it because I was curious. -Justin Quoting Justin A. Lemkul [EMAIL PROTECTED]: Nelson, A long while back, a member of our lab contemplated simulating a phosphorylated protein, but ran into some issues as well. I tried to help him by editing the ffG43a1p files, and I seem to remember making some headway. If you'd like, you can send me your .pdb file (off-list) and I'll test it against my ffG43a1p files. If it works, I can send you my modifications. I made no changes to the force field parameters, only the formatting of the files themselves. -Justin Quoting Nelson Cotrim [EMAIL PROTECTED]: Hi Justin, Thanks for the reply. Yes, I used PRODRG Beta. Thanks for the heads up about the charges. The error I got using ffG43a1 was this: Fatal error: wrong format in input file ffG43a1p.hdb on line 2 7 OW which was also described here: http://www.gromacs.org/pipermail/gmx-users/2007-August/028977.html but that did not solve my problem. I removed all the unnecessary entries from the hdb file, keeping only the SEP and P data, and then there was another error in yet another ffG43a1p file (I don't remember which one right now). I removed all ffG43a1p files and rolled back the files changed by ffG43a1p to the original ones from Gromacs 3.3.1 and tried PRODRG. So far, everything is going smoothly - I am running the dynamic even so (it's a small one, takes me just two days of computer time and there are no other MDs to run), to make sure everything goes right - the PO3 keeps its tetrahedrical shape, grompp and mdrun runs smoothly... I just will not be able to use the results because there is this extra hydrogen atom which I do not know how to remove from the .gro and .top files. Nelson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
