Re: [gmx-users] Topology Manipulation question
Hi! you usually get that type of output when the order in which the molecule atoms are written in the topology file (in the itp in your case) does not correspond to the order in the gro file; it might just be that you call the itp corresponding to the second molecule written inthe gro file before calling the itp corresponding to the first one. grompp absolutely needs the same order for the atoms to match them correctly. hope it helps, regards, Giovanna On 8/21/06, Marc Charendoff [EMAIL PROTECTED] wrote: Hello,I'm running grompp on two small molecules in a single.gro file using the following topology file: #include ffgmx.itp#include BDEX.ITP#include AHL.ITP#include spc.itp[ system ]BDEXAHL[ molecules ]BDEX 1AHL 1 Part of my output looks like the following:Back Off! I just backed up mdout.mdp to./#mdout.mdp.2#checking input for internal consistency...calling cpp...processing topology...Generated 1284 of the 1485 non-bonded parameter combinationsExcluding 3 bonded neighbours for BDEX1Excluding 3 bonded neighbours for AHL 1processing coordinates...WARNING 1 [file topol.top, line 12]:Bad box in file Complex.GRO Generated a cubic box 20.000 x1.445 x1.830Warning: atom names in topol.top and Complex.GRO don'tmatch (O2 - CAS)Warning: atom names in topol.top and Complex.GRO don'tmatch (HAA - CAR)Warning: atom names in topol.top and Complex.GRO don'tmatch (C2 - CAQ)Warning: atom names in topol.top and Complex.GRO don'tmatch (C3 - CAP)Warning: atom names in topol.top and Complex.GRO don'tmatch (O3 - CAO)Warning: atom names in topol.top and Complex.GRO don'tmatch (HAB - CAN)Warning: atom names in topol.top and Complex.GRO don'tmatch (C4 - CAM)Warning: atom names in topol.top and Complex.GRO don'tmatch (O4 - CAL)Warning: atom names in topol.top and Complex.GRO don'tmatch (C5 - CAK)Warning: atom names in topol.top and Complex.GRO don'tmatch (C6 - CAJ)Warning: atom names in topol.top and Complex.GRO don'tmatch (O6 - OAT)Warning: atom names in topol.top and Complex.GRO don'tmatch (HAC - CAI)Warning: atom names in topol.top and Complex.GRO don'tmatch (O5 - CAH)Warning: atom names in topol.top and Complex.GRO don'tmatch (C1 - OAU)Warning: atom names in topol.top and Complex.GRO don'tmatch (O1 - N)Warning: atom names in topol.top and Complex.GRO don'tmatch (CAJ - HAA)Warning: atom names in topol.top and Complex.GRO don'tmatch (CAK - CA)Warning: atom names in topol.top and Complex.GRO don'tmatch (OBY - CB)Warning: atom names in topol.top and Complex.GRO don'tmatch (CAL - CAA)Warning: atom names in topol.top and Complex.GRO don'tmatch (OBZ - OAC)(more than 20 non-matching atom names) WARNING 2 [file topol.top, line 12]:120 non-matching atom namesatom names from topol.top will be usedatom names from Complex.GRO will be ignored- Complex.GRO consists of two molecules AHL and BDEX. -The ffgmx force field has already worked successfullywith the BDEX.itp and molecule,but for some reasonall but 2 of the AHL molecule atoms have the mismatchproblem. Which file do I have to modify to clear the atom name mismatch issue? The atom names in questionare identical between the Complex.gro and AHL.itpfiles, so I'm a bit confused. Any guidance you couldprovide would be appreciated.Regards,Marc ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] Freezing part of the molecules!!!
Hi!just make an index file (make_ndx) custom-defining the groups which you need to freeze, in your case the C-alpha of residues 18-42. Remember that, when you define new groups, you should delete the corresponding atoms from the group that contains all the rest of the protein atoms, if not you'll get an error saying that a particular atom belongs simultaneously to different freezing groups. Hope it helps,greetings,MGiòOn 6/7/06, Marcelo Fabricio Masman [EMAIL PROTECTED] wrote: Hi all!!! I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest. For example, my protein group has 5 protein chains with 42 residues each of them. I would like to freeze (in all directions) the alfa Carbon atoms for residues 18-42 for each chain. Does somebody know if it is possible to do such thing with GROMACS? Can somebody help me? Thanks a lot, in advance Marcelo ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] atomtype
Hi!I'm sorry, I realize I didn't mention in my first reply that you should download the new version of ffgmx modified for describing lipids to be used with the popc.itp topology file, you can find it at this link: http://www.gromacs.org/topologies/force_fields.phpInvalid order for directive atomtypes means that you have called the various .itp files before calling the ffgmx.itp file, this way gromacs doesn't know which force field refer to when reading your topologies. The ffgmx must be the first call. Hope it helps.cheers,MGOn 5/3/06, mahbubeh zarrabi [EMAIL PROTECTED] wrote: Hi,everyone,I have tried to use popc.pdb that the coordinatesare from Tieleman's web to insert a protein.when i useffgmx.itp , there is fetal error:atomtype LC3 not found.i downloaded ffgmx_lipid but i have a problem: fetal error: invalid order for directive atomtypesfile .share\top\... line 1whould you please help me?best regardszarrabi__Do You Yahoo!? Tired of spam?Yahoo! Mail has the best spam protection aroundhttp://mail.yahoo.com___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] popc
Hi!I'm using the popc.top which I have downloaded from this websitehttp://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield. Cheers,MGOn 5/2/06, mahbubeh zarrabi [EMAIL PROTECTED] wrote: hiI try to use make_hole program to make a hole in POPC.how can i make popc.top?what is forcefield for popc ingromacs?thankszarrabi__Do You Yahoo!? Tired of spam?Yahoo! Mail has the best spam protection aroundhttp://mail.yahoo.com___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] error in pdb2gmx step
Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] error in pdb2gmx step
That means that the CO ion type is not described by the forcefield you are using, check the .rtp file of your force field or the ions.itp file in the gromacs/top directory. anyhow be careful not to make any confusion between the chain identifier, which is a 1 character id, and the residue name. Are you sure you're not shifting the columns of your pdb when deleting the chain identifier (chain A shoud be replaced by a blank)? MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Well thank you.Yes I did find a region in which chain identifier 'A' was repeating, this corresponded to the HETATM CO, so i tried removing the chain identifier in one case and in another one I tried shifting it to the correspoding chain, but in both cases i got the following error Fatal error: Residue 'CO' not found in residue topology database. Will be glad to hear any suggestions. Is there any other way in GROMACS to handle proteins with metal ions in it? Thank You, Annie Albin. On 3/31/06, MGiò [EMAIL PROTECTED] wrote: Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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] Re: g_hbond
Well,this was my command line:g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn and this was my screen output No option -daReading file ../../topol.tpr, VERSION 3.2.1 (single precision)Specify 2 groups to analyze:Opening library file /usr/local/share/gromacs/top/aminoacids.dat Group 0 ( System) has 25707 elementsGroup 1 ( Protein) has 2462 elementsGroup 2 ( Protein-H) has 1975 elementsGroup 3 ( C-alpha) has 247 elementsGroup 4 ( Backbone) has 741 elements Group 5 ( MainChain) has 989 elementsGroup 6 (MainChain+Cb) has 1226 elementsGroup 7 ( MainChain+H) has 1230 elementsGroup 8 ( SideChain) has 1232 elementsGroup 9 ( SideChain-H) has 986 elements Group 10 ( Prot-Masses) has 2462 elementsGroup 11 ( Non-Protein) has 23245 elementsGroup 12 ( EST) has 25 elementsGroup 13 ( SOL) has 23220 elementsGroup 14 ( Other) has 23245 elements Select a group: 1Selected 1: 'Protein'Select a group: 12Selected 12: 'EST'Checking for overlap...Calculating hydrogen bonds between two groups of 2462 and 25 atomsFound 349 donors and 692 acceptors in group 'Protein' Found 2 donors and 2 acceptors in group 'EST'Going to allocate 5709 kb of memory, and that's only the beginningtrn version: GMX_trn_file (single precision)Reading frame 0 time 0.000Will do grid-seach on 16x15x14 grid, rcut= 0.35Last frame 100 time 3000.000Found 5 different hydrogen bonds in trajectoryMerging hbonds with Acceptor and Donor swappedReduced number of hbonds from 5 to 5tested 1394 pairsAverage number of hbonds per timeframe 1.218 out of 1041 possibleAny idea? The screen output seems correct to me, but for the fact that it always says no -da option whether I use this option or not, why this?. Thanks for any help. MGiòOn 2/28/06, Anton Feenstra [EMAIL PROTECTED] wrote:MGiò wrote: Thanks, Kia, actually I have used an index.ndx file, but the output is the same. I'll try anyway with the automated procedure by the shell script. Thank you anywayThe script does exactly the same as what you do manually. SO that won'thelp... Can you send the screen output of g_hbond?--Groetjes,Anton* NOTE: New Affiliation, Phone Fax numbers (below) *_ ___ | | ||_ ,| K. Anton Feenstra || / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands|| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 || | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ || | If You See Me Getting High, Knock Me Down (RHCP)||_|___| ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].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 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
