Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
hello Justin thanks for your reply. I am unable to understand how to proceed in this tutorial. I am working on it from many days but I am unable to do. I have understood till the step. perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat this is the result which I got. Area per protein: 2 nm^2 Area per lipid: 10.4716089904762 nm^2 Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet : 10.475577244 nm^2 Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet : 10.4716089904762 nm^2 Writing Area per lipid... Done! and the minimization step after that. I get the confout.gro file. I am confused how to continue from the step perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat how many times do we need to run this command, nd with what changes and how to solvate the system ( which file ) and what will be the command ??? looking for your kind reply. please help. Thank you On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/14 12:51 PM, Anurag Dobhal wrote: how will I get to know that the system have shrunken enough, and which file I need to solvate. This is stated in the tutorial. -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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Thanking you On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Which means it's an invalid input file format and that's why you're getting a failure from InflateGRO. If file names are given different extensions, you can't just randomly change them and expect things to work. If you ran mdrun -v -deffnm em you will never get anything named confout.gro. Note that the tutorial explicitly says: Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro You didn't use default names. You told mdrun name all of my files em.* when you invoked -deffnm. If you simply ran: mdrun -s em.tpr you would get confout.gro. In any case, you should have em.gro which is what you should use to proceed. I have no idea where confout.gro.trr came from, but it's a trajectory and clearly not what needs to be used here. -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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Don't solvate the intermediate steps. It makes no physical sense. Only solvate when you have shrunk the system to an appropriate size based on APL. Regardless, the number of atoms in the system is way too small to be correct for the tutorial system. -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.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
how will I get to know that the system have shrunken enough, and which file I need to solvate. On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Don't solvate the intermediate steps. It makes no physical sense. Only solvate when you have shrunk the system to an appropriate size based on APL. Regardless, the number of atoms in the system is way too small to be correct for the tutorial system. -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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 10/2/14 12:51 PM, Anurag Dobhal wrote: how will I get to know that the system have shrunken enough, and which file I need to solvate. This is stated in the tutorial. -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.
[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. Thank you. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -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.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 7:06 AM, Anurag Dobhal wrote: Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. A .gro file is not simply something that you click on to magically open. It's just a listing of coordinates. Visualize it in VMD. Inspect its contents with a text editor. -Justin I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -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. -- == 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.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 7:06 AM, Anurag Dobhal wrote: Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. A .gro file is not simply something that you click on to magically open. It's just a listing of coordinates. Visualize it in VMD. Inspect its contents with a text editor. -Justin I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -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. -- == 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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Which means it's an invalid input file format and that's why you're getting a failure from InflateGRO. If file names are given different extensions, you can't just randomly change them and expect things to work. If you ran mdrun -v -deffnm em you will never get anything named confout.gro. Note that the tutorial explicitly says: Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro You didn't use default names. You told mdrun name all of my files em.* when you invoked -deffnm. If you simply ran: mdrun -s em.tpr you would get confout.gro. In any case, you should have em.gro which is what you should use to proceed. I have no idea where confout.gro.trr came from, but it's a trajectory and clearly not what needs to be used here. -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.
Re: [gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC
hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Thanks for your help Anurag dobhal On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/28/14 9:14 AM, Anurag Dobhal wrote: Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat but now the teminal says that Reading. Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380 is this output is expected ??? No, fatal errors like that are not expected. If EM successfully completed and wrote a confout.gro file, there should be no problem. Visualize confout.gro and make sure its contents are sane. -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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial KALP15 in DPPC
On 9/29/14 4:44 AM, Anurag Dobhal wrote: hello justin Can you please tell me how will i solvate my system. which command will i use and what will be my input and output file. Consult a basic tutorial for this information. The membrane protein tutorial assumes the user is already familiar with simple operations like 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.
[gmx-users] Regarding GROMACS Tutorial KALP15 in DPPC
Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 after that I am not able to understand wat to do and how to solvate the system. please can anyone expalin me in easy words how to proceed. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial KALP15 in DPPC
Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat and then i minimised the the system by running the command mdrun -v -deffnm em now i am unable to understand how to produce confout.gro please help how to proceed and where I am wrong. Thank you Anurag Dobhal On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 after that I am not able to understand wat to do and how to solvate the system. please can anyone expalin me in easy words how to proceed. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial KALP15 in DPPC
Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat but now the teminal says that Reading. Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380 is this output is expected ??? please guide me. Thank you On Sun, Sep 28, 2014 at 6:33 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat and then i minimised the the system by running the command mdrun -v -deffnm em now i am unable to understand how to produce confout.gro please help how to proceed and where I am wrong. Thank you Anurag Dobhal On Sun, Sep 28, 2014 at 5:37 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear users. I am doing the tutorial KALP15 in DPPC. I heve done till the command genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 after that I am not able to understand wat to do and how to solvate the system. please can anyone expalin me in easy words how to proceed. Please help Anurag Dobhal -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Regarding GROMACS Tutorial KALP15 in DPPC
On 9/28/14 9:14 AM, Anurag Dobhal wrote: Hey gromacs users I got the confout.gro file by running the command mdrun -v -deffnm em -o confout.gro and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat but now the teminal says that Reading. Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380 is this output is expected ??? No, fatal errors like that are not expected. If EM successfully completed and wrote a confout.gro file, there should be no problem. Visualize confout.gro and make sure its contents are sane. -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.
