[gmx-users] error in pdb2gmx step
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 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
Check you pdb file and see if the chain identifier A occurs at different places in the file. Pdb2gmx expects a chain to be continous, and if it isn't, it gets confused. If you have several chains, rename them accordingly. Cheers /Per Annie Albin 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 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 -- Per Larsson PhD Student Stockholm Bioinformatics Center +46 (0) 8 55378577 +46 (0) 733 461467 [EMAIL PROTECTED] www.sbc.su.se ___ 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
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 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
[gmx-users] Re: gmx-users Digest, Vol 23, Issue 99
hi all, my gromacs is giving me this LINC ERROR.i found in the mailing list about this and found two suggestion, one to define it as dflexible and another to increase the tau_p to 20(my initial was 0.5).I did increase it step by step in some 20 runs, still the problem persists.the LINC error is right from 0th step.Can any one help me out on this. here are my pr.mdp and md.mdp files, thanks in advance, cheers hayagreevan ___Get the FREE email that has everyone talking at http://www.mail2world.com Unlimited Email Storage POP3 Calendar SMS Translator Much More! md.mdp Description: Binary data pr.mdp Description: Binary data ___ 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
[gmx-users] (no subject)
hi all, my gromacs is giving me this LINC ERROR.i found in the mailing list about this and found two suggestion, one to define it as dflexible and another to increase the tau_p to 20(my initial was 0.5).I did increase it step by step in some 20 runs, still the problem persists.the LINC error is right from 0th step.Can any one help me out on this. here are my pr.mdp and md.mdp files, thanks in advance, cheers hayagreevan md.mdp: define=-DFLEXIBLE ttle = LD5 cpp =/usr/bin/cpp constraints = all-bonds integrator= md dt= 0.002 nsteps= 5000 nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.2 fourierspacing ` = 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order = 4 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl= berendsen tau_t = 0.1 0.1 0.1 tc-grps =protein sol NA+ ref_t = 325 325 325 ;pressure coupling is on Pcoupl = berendsen tau_p= 10.0 compressibility = 4.5e-5 ref_p= 3.0 ;generate velocities is on at 300K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 pr.mdp title = vii cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 10 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring ; Pressure coupling is not on Pcoupl = berendsen tau_p = 15.0 ref_p = 10.0 compressibility = 4.5e-5 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ___Get the FREE email that has everyone talking at http://www.mail2world.com Unlimited Email Storage POP3 Calendar SMS Translator Much More!___ 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: Problem with simulated annealing!!!
Hi Poornima,If you can paste the entire mdp file, then it can be easy for the users to suggest you things.Cheers,On 3/31/06, poornima Gajendrarao [EMAIL PROTECTED] wrote:Dear Bruce, Thank you very much for your suggestion.I tried as you said. But the only difference Which Isaw is that the temperautre goes upto 314 (I tried itwith 10ps MDrun). After that I tried for 100ps MDrun. I used the same parameters which you have mentioned inthe previous mail. I didnt change anything. And whilerunning the grompp program for simulated annealing..I am getting these warnings:ARNING 1 [file full.mdp, line unknown]:Unknown left-hand coulomb type in parameter fileWARNING 2 [file full.mdp, line unknown]:Unknown left-hand anneaing in parameter fileWARNING 3 [file full.mdp, line unknown]: Unknown left-hand anneling_npoints in parameter filecan any one help to solve this problem!!Thanks in advance.with prayers,Poornima--- [EMAIL PROTECTED] wrote: Hi Poornima, It could be that you are defining two energy/temperature groups: tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL but then only defining annealing protocols for one group: ;simulated annealing anneling = single anneling_npoints = 5 anneling_time = 2 4 6 8 10 anneling_temp = 320 338 350 360 370 I think it should be like this: annealing = single single annealing_npoints = 5 5 annealing_time = 2 4 6 8 10 2 4 6 8 10 annealing_temp = 320 338 350 360 370 320 338 350 360 370 Have a look at the mdp options part of the online manual and check the SA part. Cheers, Bruce -- Dr. Bruce F. Milne PhD CEQOFFUP Faculdade de Farmácia Universidade do Porto Rua Aníbal Cunha - 164 4050-047 Porto Portugal This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing list gmx-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__Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com___gmx-users mailing listgmx-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-- Viswanadham Sridhara,Graduate Research Assistant, Old Dominion University,Norfolk, VA-23529. ___ 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
[gmx-users] Non-zero system charge
Hello everyone, I am using PME to handle electrostatics. What happens if I run a simulation with a non-zero net charge? Does GROMACS automatically provide some sort of background charge to neutralize the system? Thanks, Bob Johnson ___ 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] Non-zero system charge
My understanding is yes. But I think it is still customary to include counterions unless you have some good reason for not doing so. Otherwise, it uses (I think) a uniform background neutralizing charge. On 3/31/06, Bob Johnson [EMAIL PROTECTED] wrote: Hello everyone, I am using PME to handle electrostatics. What happens if I run a simulation with a non-zero net charge? Does GROMACS automatically provide some sort of background charge to neutralize the system? Thanks, Bob Johnson ___ 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 ___ 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
