[gmx-users] Issue with protein-ligand simulation
Dear all, I am trying to run a protein-ligand simulation as described in the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/01_pdb2gmx.html However, while creating a unit cell using editconf command, I encounter a problem. The output file (box.gro) doesn't contain the ligand coordinates. The command doesn't give any error and runs smoothly. But, when I reach the energy minimization step, grompp command gives the "Number of coordinates in coordinate file does not match topology" error. Kindly suggest how to fix this issue. Thank you. Regards, Gayathri S. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in creating parameter files using SwissParam
Dear GROMACS users and developers, I want to run MD simulation of a protein bound to FAD using CHARMM36 force field. However, I need to generate the parameter files of FAD first. Hence, I followed the following steps: 1. Downloaded the .pdb structure file from RCSB PDB databank 2. Kept the coordinates of FAD and deleted the rest 3. Added H-atoms and converted to .mol2 file using UCSF Chimera (as suggested in the website) 4. Submitted this file as input in the SwissParam site Error obtained Thank you for using SwissParam. Unfortunately, topology and parameters were not successfully generated for 3w2g_fad. A failure report can be found below. Failure report: Possible problem with molecular topology in 3w2g_fad.mol2. SwissParam will try to reconstruct the topology from coordinates only. Topology and parameters were NOT generated. Please check the validity of your molecule. - Are all hydrogens present in the mol2 file? - Is the mol2 file correct? Please, read "How to obtain a correct mol2 file?" in the www.swissparam.ch website. Kindly suggest how I can resolve the issue. Thank you. Regards, Gayathri S -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Calculating the radius of gyration of clusters
Dear all, I ran MD simulations of a small molecule and clustered structurally similar frames together. I wanted to find the radius of gyration of all the members of each cluster. To do the same, I used the command: $ g_gyrate -f cluster.xtc -s full.tpr -o cluster_rg.xvg Here, the file "cluster.xtc" was obtained as output from the g_cluster command. When I ran the above command, I got the following error multiple times: There were 10 inconsistent shifts. Check your topology. Is there a better way of finding the radius of gyration of all the cluster members in a given cluster? Please suggest how I should go about. Thank you Regards, Gayathri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Magic number error in XTC file
Hi Tsjerk, Thank you for your help. I tried what you had asked me to do: $trjconv -f production_1.trr -o production_1.xtc -n index.ndx Then, I selected the entire system from the index file. However, when I used gmxcheck to verify the output file production_1.xtc, I got the following error: Fatal error: No XTC! Please suggest how to resolve this issue. Thank you. Regards, Gayathri > Hi Gayathri, > > For the XTC file you used only a selection of atoms to write out. The TRR > file always contains everything. With the conversion from TRR to XTC make > sure to write the same selection as is in the other XTC files. > > Hope it helps, > > Tsjerk > > On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S <gayathr...@iitb.ac.in> wrote: > >> Dear all, >> >> I had a run an MD simulation (GROMACS 4.6.6) which was abruptly stopped >> due to power failure. Then, I extended the simulation using the >> commands: >> >> $tpbconv -s production.tpr -o production_2.tpr -untill 5 >> >> $mdrun -v -s production_2.tpr -deffnm production_2 -cpi production.cpt >> >> Then, when the simulation was complete, I renamed the output files of >> the >> first simulation as production_1. Next, I wanted to merge the >> trajectories >> of both the runs; hence, I used the following command: >> >> $trjcat -f production_1.xtc production_2.xtc -o production.xtc >> -overwrite >> >> Fatal Error: Magic number error in XTC file >> >> When I went through the mailing list archive, I found that this error is >> shown when the trajectory is corrupted. >> So, I used gmxcheck to find out which of the trajectories were >> corrupted. >> I discovered that production_1.trr did not show any error, but >> production_1.xtc showed the same error. >> Hence, I used trjconv to make a new production_1.xtc >> >> $trjconv -f production_1.trr -o production_1.xtc >> >> Again, I checked the new file for error using gmxcheck. When everything >> looked good, I tried the trjcat command again, only to get the following >> error >> >> Fatal error: Different numbers of atoms (584885/9944) in the files. >> >> Please suggest how to resolve the issue. >> >> Thank you. >> >> Regards, >> Gayathri. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Magic number error in XTC file
Dear all, I had a run an MD simulation (GROMACS 4.6.6) which was abruptly stopped due to power failure. Then, I extended the simulation using the commands: $tpbconv -s production.tpr -o production_2.tpr -untill 5 $mdrun -v -s production_2.tpr -deffnm production_2 -cpi production.cpt Then, when the simulation was complete, I renamed the output files of the first simulation as production_1. Next, I wanted to merge the trajectories of both the runs; hence, I used the following command: $trjcat -f production_1.xtc production_2.xtc -o production.xtc -overwrite Fatal Error: Magic number error in XTC file When I went through the mailing list archive, I found that this error is shown when the trajectory is corrupted. So, I used gmxcheck to find out which of the trajectories were corrupted. I discovered that production_1.trr did not show any error, but production_1.xtc showed the same error. Hence, I used trjconv to make a new production_1.xtc $trjconv -f production_1.trr -o production_1.xtc Again, I checked the new file for error using gmxcheck. When everything looked good, I tried the trjcat command again, only to get the following error Fatal error: Different numbers of atoms (584885/9944) in the files. Please suggest how to resolve the issue. Thank you. Regards, Gayathri. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees
Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. To achieve the same, I used the following command: $g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral I got the desired output. However, the output shows angles ranging from -180 degrees to +180 degrees. Is it possible to get the same output in 0 to 360 degrees format? If yes, what command should be used and in what syntax should it be used? Please suggest how to proceed. Thank you. Regards, Gayathri. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees
Thank you very much.
That was helpful.
Regards,
Gayathri S.
> Hi,
>
> I'm assuming you are measuring more than one dihedral (since you are using
> the -all option). So assuming columns 2 to 5 correspond to the measured
> dihedrals:
>
> awk '{print $1,($2+180),($3+180),($4+180),($5+180)}' angaver.xvg > new_
> angaver.xvg
>
> This should do the trick.
>
> Regards,
>
>
> On 10 September 2015 at 08:47, GAYATHRI S <gayathr...@iitb.ac.in> wrote:
>
>> Hello everyone,
>>
>> I simulated an NADH molecule. I want to check how each of the dihedral
>> angles changes during the simulation. To achieve the same, I used the
>> following command:
>>
>> $g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral
>>
>> I got the desired output.
>> However, the output shows angles ranging from -180 degrees to +180
>> degrees.
>> Is it possible to get the same output in 0 to 360 degrees format? If
>> yes,
>> what command should be used and in what syntax should it be used?
>>
>> Please suggest how to proceed.
>>
>> Thank you.
>>
>> Regards,
>> Gayathri.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> School of Life Sciences
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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Re: [gmx-users] Using -all flag in g_angle command
Got it! Thank you. Hi, Did you look at the full contents of the output files? I expect they're in the same file produced without -all. Mark On Thu, Jan 15, 2015 at 12:47 PM, GAYATHRI S gayathr...@iitb.ac.in wrote: The following command generated only two outputs - angaver.xvg and angdist.xvg: $ g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral The -all flag is supposed to generate graphs for individual angles, but it didn't. gmx angle -h suggests -ov -all generates multiple graphs, only the first of which is the average. What's in the rest of your output file? Mark On Wed, Jan 14, 2015 at 7:21 AM, GAYATHRI S gayathr...@iitb.ac.in wrote: Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. In other words, I want to plot a graph of individual (not average) dihedral angles versus time. To do so, I created an index file using the following command: $ mk_angndx -s full.tpr -n angle.ndx -type dihedral Next, I used the g_angle command as follows: $ g_angle -f full.xtc -n angle.ndx -type dihedral -all However, this command generated only one output file angdist.xvg. The -ov flag generates angles in degrees; but, it gives values in average and I want the same plot for individual angles. Please suggest how to proceed. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using -all flag in g_angle command
The following command generated only two outputs - angaver.xvg and angdist.xvg: $ g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral The -all flag is supposed to generate graphs for individual angles, but it didn't. gmx angle -h suggests -ov -all generates multiple graphs, only the first of which is the average. What's in the rest of your output file? Mark On Wed, Jan 14, 2015 at 7:21 AM, GAYATHRI S gayathr...@iitb.ac.in wrote: Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. In other words, I want to plot a graph of individual (not average) dihedral angles versus time. To do so, I created an index file using the following command: $ mk_angndx -s full.tpr -n angle.ndx -type dihedral Next, I used the g_angle command as follows: $ g_angle -f full.xtc -n angle.ndx -type dihedral -all However, this command generated only one output file angdist.xvg. The -ov flag generates angles in degrees; but, it gives values in average and I want the same plot for individual angles. Please suggest how to proceed. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Using -all flag in g_angle command
Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. In other words, I want to plot a graph of individual (not average) dihedral angles versus time. To do so, I created an index file using the following command: $ mk_angndx -s full.tpr -n angle.ndx -type dihedral Next, I used the g_angle command as follows: $ g_angle -f full.xtc -n angle.ndx -type dihedral -all However, this command generated only one output file angdist.xvg. The -ov flag generates angles in degrees; but, it gives values in average and I want the same plot for individual angles. Please suggest how to proceed. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off
Thank you for your suggestions. I followed your instruction and applied potential modifier during energy minimization. However, the problem still persists. Please suggest what to do. On 9/26/14 5:34 AM, GAYATHRI S wrote: Hello everyone, I'm running a simulation with Verlet scheme (for GPU). I've used cut-off method for van der Waals interactions and PME for electrostatic interactions. For energy minimization, I used steepest descent, conjugate gradient and l-bfgs sequentially. However, when I come to BFGS minimization, I get the following warning: Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off Did you use a suitable vdw-modifier? Perhaps some of the input checking is still out of whack, but if not, a suitable modifier should take care of this. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off
Hello everyone, I'm running a simulation with Verlet scheme (for GPU). I've used cut-off method for van der Waals interactions and PME for electrostatic interactions. For energy minimization, I used steepest descent, conjugate gradient and l-bfgs sequentially. However, when I come to BFGS minimization, I get the following warning: Warning: For efficient BFGS minimization, use shift/switch/PME instead of cut-off When I changed the cut-off to shift for vdW interactions as per the warning, I get error: With Verlet lists only cut-off LJ interactions are supported. Please help. Thanking you, Gayathri S. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
