[gmx-users] Restrict Terminal of protein?
Dear user: I am do a complex simulation,recepter is big protein,So I cut a domain of it to simulation, when I simulation, the terminal of receptor(cut) disordered, So I want to restrict it,just fix it on a point, Could somebody tell me how to do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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:isotropic force constant
Thank you for your advice,I have find define=-DPOSRE in my pr.mdp file, but I don't know which parameter indicate isotropic force constant of 100kjmol-1A-1. Though I use ref_t=300 for my simulation. Dear users: I have a position restrain .mdp file need to set,I use 300K in which an isotropic force constant of 100kjmol-1A-1 is applied to all nonhydroggen protein atoms. In my pr.mdp file which parameter I should add? Thank you very much! If you use pdb2gmx, it will generate a posre.itp file which you can modify to do whatever you want (although I think the above might be the default). See the manual for details on how. Then to make it work, the .mdp file needs to have 'defines = -DPOSRE' or something similar - check manual section 7.3. Mark ___ 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] isotropic force constant?
Dear users: I have a position restrain .mdp file need to set,I use 300K in which an isotropic force constant of 100kjmol-1A-1 is applied to all nonhydroggen protein atoms. In my pr.mdp file which parameter I should add? Thank you very much! ___ 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] Salt concentration!
Dear users: My protein is large,so I use genbox -shell 1.2 to add water, Then I genion -conc 0.15 -neutral, At last,In .top file I find 7703 water, but there are 183 Na+,170 cl-,I want to know whether ions is too more. Is this normal? Could somebody tell me? ___ 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:realloc Error !
Mark: Thank you for your advice,I always get one of these error message, in same situation. I find that when I got box shift error message,there are many lincs warning. I did not find some special message for memory not enough error message. Qiang Zhong : I have a complex protein which is predicted from cluspro server,I use it as a start structure,I want to know the complex will deformated to a new conformation which is NMR experiment result(it only include a fragment of protein).So I want to know the two protein interaction information by MD. I use energy minimize step to get optimize structure,but there Fmax always 1.So I don't know how to do! You need an adequately minimized structure, but you won't be able to get Fmax of zero. Adequate just means that later when you heat the system and do your equilibration run that things do not fall apart. Otherwise,I got another error message in same situation: Fatal error: Box was shifted at least 10 times. Please see log-file. When? During the minimization? What was different between when you got this error message and when you didn't? I also don't know how to understand it. Could you tell me reason?Thank you very much! Please be aware that in typed English, spaces are used after punctuation marks like commas, periods and interrogation marks (i.e. ',', '.', '?') in order to make the text easier to read. Mark ___ 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:realloc Error !
I have a complex protein which is predicted from cluspro server,I use it as a start structure,I want to know the complex will deformated to a new conformation which is NMR experiment result(it only include a fragment of protein).So I want to know the two protein interaction information by MD. I use energy minimize step to get optimize structure,but there Fmax always 1.So I don't know how to do! Otherwise,I got another error message in same situation: Fatal error: Box was shifted at least 10 times. Please see log-file. I also don't know how to understand it. Could you tell me reason?Thank you very much! Dear users: I simulate a large system which are 27062 atoms (include water),after mdrun hours,I receive a error message: Fatal error: realloc for grid-nra (-410897240 bytes, file nsgrid.c, line 159, grid-nra=0x0x 8cd3200) Could somebody tell me what wrong with it,what should I do? Thank you very much! Probably, equilibrate the system better. You'd need to tell us more about what you're doing in order to get a better guess, however. Mark ___ 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] realloc Error !
Dear users: I simulate a large system which are 27062 atoms (include water),after mdrun hours,I receive a error message: Fatal error: realloc for grid-nra (-410897240 bytes, file nsgrid.c, line 159, grid-nra=0x0x 8cd3200) Could somebody tell me what wrong with it,what should I do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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] genion error!
Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Fatal error: Too many LINCS warnings (10190) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. I don't know what happen ,could somebody tell me? Thank you very much! pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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] Add ions on protein
Hellow: I have a protein which have 4 calcium ions binding sites,Now I have the free calcium ions protein, I want to add calcium ions on the binding sites,but I know the free ions protein conformation is very different to ions loaded protein. So I want to know whether there is some way to let complex of protein and ions to a native ca2+ loaded conformation. Could somebody tell me how to do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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] LINCS WARNING
Hellow : I am runing a MD of protein. Now I see some warning message on screen,I don't know how to understand it , Could somebody tell me about it? Thank you very much! bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931932 33.00.1001 0.1000 0.1000 Step 1535921, time 3071.84 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001443 (between atoms 931 and 932) rms 0.50 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 30.50.1001 0.1000 0.1000 Step 1535922, time 3071.84 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001952 (between atoms 931 and 933) rms 0.62 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 35.20.1000 0.1000 0.1000 Step 1535923, time 3071.85 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001902 (between atoms 931 and 933) rms 0.60 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 33.40.1000 0.0999 0.1000 .. What happen with it,Is this harm to my result? -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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] How to display file .xvg,how to use my_dssp
Hollow: My linux can not instal grace,so I don't know to view .xvg file,Could someone tell me some other graphic software. I want to use my_dssp , but I don't know where it is,Could someone tell me where to find it? -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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] Error:4 atoms are not part of any of the T-Coupling groups
Hollow: I have post my question last time,my emailbox can not work, So I post again. I have 4 calcium ions bind at protein, when I use command: grompp -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr I got error message: Fatal error: 4 atoms are not part of any of the T-Coupling groups I got a advice to use : make_ndx -f minimized_water.gro Then I got a file index.ndx I find the line in index.ndx ,just like below: 57378 57379 57380 57381 [ CA ] 1234 [ SOL ] Then I delete them,and run again: grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr But Error still there. Could somebody tell me how to do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ 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:Error:4 atoms are not part of any of the T-Couplinggroups
I have solved this problem by all your advices. Thank you, Mark and Yang Ye for your help! That wasn't the advice Yang Ye gave you... see http://www.gromacs.org/pipermail/gmx-users/2007-February/025792.html For a simpler solution, see http://www.gromacs.org/pipermail/gmx-users/2007-February/025796.html Mark Message: 6 Date: Wed, 07 Feb 2007 22:29:36 +0800 From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] Error:4 atoms are not part of any of the T-Coupling groups To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Interesting that you have your Ca2+ ions in the beginning of your structure file. In this case, remove the line [ SOL ] and replace [ CA ] with [ SOL ]. Although, changing your mdp file to have Protein Non-Protein is simpler. The rationale behind is that the *groups* included for the tc-grps shall cover all atoms. On 2/7/2007 9:34 PM, Qiang Zhong wrote: Hollow: I have post my question last time,my emailbox can not work, So I post again. I have 4 calcium ions bind at protein, when I use command: grompp -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr I got error message: Fatal error: 4 atoms are not part of any of the T-Coupling groups I got a advice to use : make_ndx -f minimized_water.gro Then I got a file index.ndx I find the line in index.ndx ,just like below: 57378 57379 57380 57381 [ CA ] 1234 [ SOL ] Then I delete them,and run again: grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr But Error still there. Could somebody tell me how to do? Thank you very much! ___ 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
