Re:Re: [gmx-users] copper and His residues
-- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden At 2012-01-04 04:04:46,"Justin A. Lemkul" wrote: > > >xianqiang wrote: >> You do not need to fix the copper in the calculation. There are must be >> some negative charged residues around the copper. Therefore, the copper >> will located at the place where it should be. >> > >I agree that a position restraint on copper is not appropriate, but I strongly >disagree with the assumption that it will simply be held in place by virtue of >negative charges. I know of many cases where the MM approximations and >electrostatic interactions were insufficient to preserve active-site geometry. >There are a number of QM/MM studies that have concluded that fixed point >charges >on such species suffer from many limitations, not the least of which are >inductive effects and the inability to account for orbital geometry. A series >of distance restraints between ligating residues and the copper ion itself may >be the best approach for "standard" MD simulations. > >-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 > I agree your opinion on some degree. But I think he should do the simulation with the copper at reasonable place without restraint at first. If it is not work, the electrostatic interaction may be not strong enough for locating the copper. Then, he can redo the calculation with distance restraint between the copper and residues nearby. So the choice should depend on the system he worked on. regards > >-- >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] copper and His residues
You do not need to fix the copper in the calculation. There are must be some negative charged residues around the copper. Therefore, the copper will located at the place where it should be. regards. -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden At 2012-01-04 01:15:34,ljin1988 wrote: Hello, I am a beginner of Gromacs, and I am working with enzyme that contains two Cu2+ ions in the active site. I have found two solution to treat copper ions and surrounding His residues. First solution is adding position restrain to these ions, while the second one is defining bonds between copper ions and surrounding His residues. I just wonder about which one should I adopt? Thanks very much. -- 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:Re: [gmx-users] MDRun -append error
Hi Roland,
Thanks for your reply. My log files are located in the same directory with
''traj.xtc', and the log files are readable by gromacs.
I have just find out the solution for my problem. That is because there were
also two backup log files named '#md_0_1.log#' and '#md_0_1.edr#' corresponding
to 'md_0_1.log' and 'md_0_1.edr'. These two files were generated for a trial
run. After removing the two files ('#md_0_1.log#' and '#md_0_1.edr#), gromacs
can restart successfully.
Thanks for your reply!
best regards
Xianqiang
--
Xianqiang Sun
Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
S-106 91 Stockholm, Sweden
在 2011-11-17 09:12:25，"Roland Schulz" 写道：
On Wed, Nov 16, 2011 at 4:11 PM, xianqiang wrote:
Hi, all
I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi
state.cpt -append'
However, the following error appears:
Output file appending has been requested,
but some output files listed in the checkpoint file state.cpt
are not present or are named differently by the current program:
output files present: traj.xtc
output files not present or named differently: md_0_1.log md_0_1.edr
---
Program mdrun, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139
Fatal error:
File appending requested, but only 1 of the 3 output files are present
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The two files which can not be found were located in the same directory with
'traj.xtc', and why they can not be found by gromacs?
Maybe they are not readable? Can you look at the log file (e.g. using "less")?
Roland
Thanks and best regards,
Xianqiang
--
Xianqiang Sun
Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
S-106 91 Stockholm, Sweden
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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[gmx-users] MDRun -append error
Hi, all I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi state.cpt -append' However, the following error appears: Output file appending has been requested, but some output files listed in the checkpoint file state.cpt are not present or are named differently by the current program: output files present: traj.xtc output files not present or named differently: md_0_1.log md_0_1.edr --- Program mdrun, VERSION 4.5.3 Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139 Fatal error: File appending requested, but only 1 of the 3 output files are present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The two files which can not be found were located in the same directory with 'traj.xtc', and why they can not be found by gromacs? Thanks and best regards, Xianqiang -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden -- 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] restart the mdrun with the checkpoint file
Dear all, I am trying to use the checkpoint file for the MDrun which war crashed. However, the following error file was obtained in my log file: Reading file md_0_2.tpr, VERSION 4.5.5 (single precision) Reading checkpoint file state.cpt generated: Tue Nov 8 08:06:42 2011 starting mdrun 'Protein in water' 2000 steps, 2.0 ps (continuing from step 1685550, 1685.5 ps). [a02c31n06.pdc.kth.se:20072] 7 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics [a02c31n06.pdc.kth.se:20072] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages --- Program mdrun, VERSION 4.5.3 Source code file: ../../../gromacs-4.5.3/src/gmxlib/futil.c, line: 459 File input/output error: state_step1714850.cpt For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Good Music Saves your Soul" (Lemmy) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 gcq#311: "Good Music Saves your Soul" (Lemmy) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 0 with PID 20073 on node a02c31n06.pdc.kth.se exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- ~ Anyone can help me with this problem? Thanks so much, Xianqiang -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden -- 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
