Re: [gmx-users] Help with Error Message
What kind of editor should I open it in? I have Pymol, but I don't know if it's the right one. -- 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] Help with Error Message
I've moved on from that point; now I'm stuck at where it asks me to remove molecules of solvent from the topology file. On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar wrote: > Hey :) > > Sorry for replying a bit late. But the issues you mention in this and the > other posts are usually solved by closely reading the text of the tutorial, > not only the commands. > > Cheers, > > Tsjerk > > > On Sun, Aug 25, 2013 at 3:44 AM, The One And Only >wrote: > > > Never mind, I'm dumb. I just realized that protein.pdb means i have to > > specify which protein i want like "1qlz.pdb" and not actually type > > "protein.pdb" BUT THANKS GUYS!! > > > > > > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only > >wrote: > > > > > so how do i solve the protein.pdb issue? > > > > > > > > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul > wrote: > > > > > >> > > >> > > >> On 8/24/13 9:26 PM, The One And Only wrote: > > >> > > >>> that's something i know nothing about; I just graduated from high > > school > > >>> and I have no background or experience in open source projects or > > >>> programs > > >>> like pymol/gromacs. My professor wants me to be able to produce a > > setup, > > >>> simulation, and analysis within a week so I'm pretty desperate right > > now > > >>> in > > >>> terms of getting help. Do you know how to get the right .pdb file in > my > > >>> working directory? > > >>> > > >>> > > >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux > > >> tutorial. Google can find lots of good ones. Producing a quality > > >> simulation cannot be rushed, and if you don't know the fundamentals of > > >> navigating the command line and directory structure, it's nearly > > >> impossible. You need to invest time in learning the environment > before > > >> doing anything, I'm afraid. Just to give a bit of perspective, we > used > > to > > >> train our undergrads for nearly a full semester (at least 2-3 months) > > >> before requiring them to do any "real" work. At least a week or two > of > > >> that time was spent getting used to command line and Linux in general. > > >> > > >> -Justin > > >> > > >> -- > > >> ==** > > >> > > >> Justin A. Lemkul, Ph.D. > > >> 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 > > >> > > >> jalemkul@outerbanks.umaryland.**edu < > jalem...@outerbanks.umaryland.edu>| > > (410) > > >> 706-7441 > > >> > > >> ==** > > >> -- > > >> gmx-users mailing listgmx-users@gromacs.org > > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > >> * Please search the archive at http://www.gromacs.org/** > > >> Support/Mailing_Lists/Search< > > 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< > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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] #coordinates do not match
How do you decrease the number of solvent molecules in a topology file? I think this will solve my problem. On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan wrote: > Hi, > In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral > -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I > don't think the ions are written into your .top . Please check and see if > grompp works. > > > On Sun, Aug 25, 2013 at 9:34 AM, The One And Only >wrote: > > > I've tried the same process twice to two different proteins, but still > got > > the same error that the #coordinates in the topology file did not match > the > > #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is > > the process I went through: > > > > *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* > > > > *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* > > > > *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* > > > > *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* > > > > *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* > > > > *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* > > > > *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname > > NA -nname CL* > > > > *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o > > 1xyw-EM-solvated.tpr* > > -- > > 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 > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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
[gmx-users] #coordinates do not match
I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh* *grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr* *mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd* *editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0* *genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb* *grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr* *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* *grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o 1xyw-EM-solvated.tpr* -- 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] Ok now what?
I've been able to set up everything correctly according to the tutorial I found on the website. I got the following error when I typed: grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 141 of the 1176 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file 1qlz.top, line 7226]: System has non-zero total charge: -2.99 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. processing coordinates... --- Program grompp, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (1qlz-solvated.pdb, 24574) does not match topology (1qlz.top, 24672) I'm stuck. -- 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] Help with Error Message
Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like "1qlz.pdb" and not actually type "protein.pdb" BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only wrote: > so how do i solve the protein.pdb issue? > > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul wrote: > >> >> >> On 8/24/13 9:26 PM, The One And Only wrote: >> >>> that's something i know nothing about; I just graduated from high school >>> and I have no background or experience in open source projects or >>> programs >>> like pymol/gromacs. My professor wants me to be able to produce a setup, >>> simulation, and analysis within a week so I'm pretty desperate right now >>> in >>> terms of getting help. Do you know how to get the right .pdb file in my >>> working directory? >>> >>> >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux >> tutorial. Google can find lots of good ones. Producing a quality >> simulation cannot be rushed, and if you don't know the fundamentals of >> navigating the command line and directory structure, it's nearly >> impossible. You need to invest time in learning the environment before >> doing anything, I'm afraid. Just to give a bit of perspective, we used to >> train our undergrads for nearly a full semester (at least 2-3 months) >> before requiring them to do any "real" work. At least a week or two of >> that time was spent getting used to command line and Linux in general. >> >> -Justin >> >> -- >> ==** >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> jalemkul@outerbanks.umaryland.**edu | >> (410) >> 706-7441 >> >> ==** >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<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] Help with Error Message
so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul wrote: > > > On 8/24/13 9:26 PM, The One And Only wrote: > >> that's something i know nothing about; I just graduated from high school >> and I have no background or experience in open source projects or programs >> like pymol/gromacs. My professor wants me to be able to produce a setup, >> simulation, and analysis within a week so I'm pretty desperate right now >> in >> terms of getting help. Do you know how to get the right .pdb file in my >> working directory? >> >> > Rudimentary Unix commands like cp and mv are covered in any Unix/Linux > tutorial. Google can find lots of good ones. Producing a quality > simulation cannot be rushed, and if you don't know the fundamentals of > navigating the command line and directory structure, it's nearly > impossible. You need to invest time in learning the environment before > doing anything, I'm afraid. Just to give a bit of perspective, we used to > train our undergrads for nearly a full semester (at least 2-3 months) > before requiring them to do any "real" work. At least a week or two of > that time was spent getting used to command line and Linux in general. > > -Justin > > -- > ==** > > Justin A. Lemkul, Ph.D. > 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 > > jalemkul@outerbanks.umaryland.**edu | > (410) > 706-7441 > > ==** > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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] Help with Error Message
that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in terms of getting help. Do you know how to get the right .pdb file in my working directory? On Sat, Aug 24, 2013 at 6:23 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > It sounds like you dont have the .pdb file in your working directory. > Perhaps you need to learn a bit about unix filesystems > > > On Sat, Aug 24, 2013 at 6:18 PM, The One And Only >wrote: > > > So I started following some tutorials online since I didn't get a > response > > last time. the tutorial I'm using is: > > http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ > > I followed that tutorial to the second page and got stuck at the step > where > > it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p > protein.top > > -ignh > > I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for > > the water model but got the following error message: > > Opening force field file > > /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b > > Reading protein.pdb... > > > > --- > > Program pdb2gmx, VERSION 4.6.3 > > Source code file: > > /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 > > > > File input/output error: > > protein.pdb > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > Help please? > > -- > > 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 > -- 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] Help with Error Message
So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for the water model but got the following error message: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b Reading protein.pdb... --- Program pdb2gmx, VERSION 4.6.3 Source code file: /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 File input/output error: protein.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Help please? -- 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
