[gmx-users] protein falls apart in energy minimization
hi all I am running Gromacs on a protein consisted of three chains. But no matter how I tried, the protein always falls into three parts (corresponding to each chain) after a simple 2000 steps energy minimization. Can anyone help me please? Thanks. Zhong Zheng ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Questions about energy groups!
Dear all I have successfully run though the energy minimization on my target protein. I am trying to extract the backbone-backbone interactions from the energy output files. My understanding is that I need to define the energy groups in the grompp.mdp. This is what I edited: energygrps = mainchain I also have the index file ready. mainchain is defined in it which is actually a default group. However I am getting the following error message when I move on to run grompp (grompp -n *.ndx) : atoms 1 and 2 in charge group 1 of molecule type 'Protein_L' are in different energy groups Atom 12 are the N and H1 in an Ala. They are defined in one charge group. If I manually modify the topol file and make them into different charge groups, the program will move on and complain about another two atoms. However, the backbone atoms (N C CA O) ARE put in different charge group in the opls force field I am using. So my questions are: 1. Can I extract the backbone-backbone interactions directly using g_energy or some other commands? 2. How can I fix this error? Do I have to put all the backbone atoms in the same charge group? Many thanks. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE new wiki: http://134.74.90.158/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atom H is missing in the first residue in a chain
Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c- terminus? How can I fix this? Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option -missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 gmx-users-requ...@gromacs.org. 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 jalemkul[at]vt.edu | (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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N- terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option - missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 gmx-users-requ...@gromacs.org. 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 jalemkul[at]vt.edu | (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 gmx-users-requ...@gromacs.org. 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 jalemkul[at]vt.edu | (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 gmx-users-requ...@gromacs.org. 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 jalemkul[at]vt.edu | (540
[gmx-users] How to treat an isolated iron (Fe 2+)
hi all I have an isolated iron in the protein. If I don't' put that iron in, everything runs through fine. However, if I put the iron in, the mdrun step (doing energy minimization) will clash. It says segmentation fault and lots of LINCS WARNING. The iron has a +2 charge with four His ligands and one Glu ligand. The total charge for the complex should be +1. Is there a good way to treat this isolated iron? Thanks a lot. Zhong Zheng ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom H is missing in the first residue in a chain
Thanks Justin. I fixed it this time. I basically renamed the terminal residues. The reason it didn't work last time is probably because some format problem. Thanks again. On Jan 14, 2009, at 2:50 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so, i tried already and still not working. Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the correct Amber residue names for all other amino acids in your structure (i.e., C-terminal residues, histidines, etc). An easy way might be to process your .pdb with xLeap (now free as part of AmberTools), and use the output .pdb as your input into pdb2gmx. Have you carefully followed all instructions here: http://chemistry.csulb.edu/ffamber/#usage Have you updated your aminoacids.dat appropriately (see above link)? -Justin On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote: Please keep all correspondence on the list. Zhong Zheng wrote: Yes. Amber. Gromacs Version 4.0.2. It's compiled on my computer, macbook. I followed standard procedure,nothing special. The Amber force fields use their own special nomenclature, so N- terminal alanine would actually be called NALA. You will have to modify your .pdb file to correspond with Amber naming conventions before this step will complete properly. -Justin On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: I tried this: pdb2gmx -f prot.pdb -ignh, not working What I am using is : pdb2gmx -f prot.pdb -missing Does the behavior occur when you process each chain separately? Which force field are you using? Which version of Gromacs are you using, and how was it compiled? I experienced the same behavior in version 3.3.1, resulting from a broken Ubuntu package. -Justin On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote: What is your exact pdb2gmx command line? -Justin Zhong Zheng wrote: hi Thanks for your reply. I tried -ignh and it doesn't help. I understand -missing is bad but I made sure the only missing atoms the program complains are the first residue in each three chains. I am using a crystal structure. However the warning messages are only for the first residue in each chain. Zhong On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote: Zhong Zheng wrote: Hi all I am running Gromacs on a three-chain protein. The program complains about atom H is missing in residue ALA 1 in the pdb file, You might need to add atom H to the hydrogen database of residue ALA in the file ff???.hdb (see the manual). It's a warning message. I can use the option - missing to ignore it. However I would like to understand this. It's always the first residue in the chain. So I am thinking this is because they are the n-terminus. Then why no complain about c-terminus? How can I fix this? Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. The problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be present in the .pdb file. If you are using a crystal structure, this requirement will not be satisfied. Likely pdb2gmx does not complain about the C-terminus because it is unprotonated, or otherwise the program exits after finding a missing N-terminal hydrogen. As an aside, using -missing is generally a very bad idea, unless you have a very specific (and anticipated!) reason to use it. -Justin Thanks a lot. Zhong Zheng Ph.D candidate Physics Dept., City College-CUNY Marshak Science Building J-419 , 160 Convent Ave, New York, NY 10031 USA Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/ MCCE http://scratchpad.wikia.com/wiki/MCCE ___ 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 gmx-users- requ...@gromacs.org. 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 jalemkul[at]vt.edu | (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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/ users.php -- Justin A. Lemkul Graduate Research Assistant
