Re: [gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)
On 3/18/15 4:05 PM, Thomas Lipscomb wrote: Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails. If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. -Justin Thanks. Strangely, charmm36.ff already had gb.itp, but what fixed that file not found error that was copying all of the files (including gb.itp) from: /usr/local/gromacs/share/gromacs/top/charmm36.ff to my working directory: /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP/charmm36_lipid.ff While not overwriting the modified files that were already in charmm36_lipid.ff I have no idea why this works. But now I am getting the error: ---Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603 Fatal error:number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6802)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- topol.top has this: [ molecules ]; Compound#molsProtein_chain_A 1DPPC 128 But the system_shrink1.gro only has the DPPC not the protein. The protein has 402 coordinates so clearly system_shrink1.gro not having the 402 protein coordinates is the problem. Do I copy the 402 protein coordinates from [ atoms ] in topol.top to system_shrink1.gro? The coordinates seem to be in different formats. Topologies are not coordinates. You need to actually construct the system correctly. If you have only DPPC, then you don't have a protein, which means you've probably forgotten to do something. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Error while shrinking lipids (KALP15 in DPPC tutorial)
Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails. If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. -Justin Thanks. Strangely, charmm36.ff already had gb.itp, but what fixed that file not found error that was copying all of the files (including gb.itp) from: /usr/local/gromacs/share/gromacs/top/charmm36.ff to my working directory: /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP/charmm36_lipid.ff While not overwriting the modified files that were already in charmm36_lipid.ff But now I am getting the error: ---Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603 Fatal error:number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6802)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors--- topol.top has this: [ molecules ]; Compound #molsProtein_chain_A 1DPPC 128 But the system_shrink1.gro only has the DPPC not the protein. The protein has 402 coordinates so clearly system_shrink1.gro not having the 402 protein coordinates is the problem. Do I copy the 402 protein coordinates from [ atoms ] in topol.top to system_shrink1.gro? The coordinates seem to be in different formats. Sincerely,Thomas -- 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] Error while shrinking lipids (KALP15 in DPPC tutorial)
On 3/17/15 12:12 AM, Thomas Lipscomb wrote:
Dear gmx-users,
I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the CHARMM36
forcefield. I think the lipid shrinking was a step I did badly last time (I think I was
getting can open em.tpr but not open em1.tpr, em2.tpr, etc.), which might be
why that run had poor lipid packing.
This is the page of the tutorial I am stuck
at:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The KALP15 in DPPC tutorial says to scale down the lipids by 0.95 for 26 times.
So I repeated this group of 3 commands 26 times:/usr/local/gromacs/bin/gmx
grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o
em.tpr/usr/local/gromacs/bin/gmx mdrun -s em.tpr -vperl inflategro.pl
confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
I am not sure what file to check to make sure doing that is right. I hope it
is.
Visualizing is a start. Are the lipids becoming more compact around the
proteins? It should be very easy to tell.
Anyway I also tried:
cp em.tpr em1.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p
topol.top -o em1.tpr/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -vperl
inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5
area_shrink2.datcp em1.tpr em2.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p
topol.top -o em2.tpr/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -vperl
inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5
area_shrink3.datcp em2.tpr em3.tpr
etc.
But then I got this error I have never seen
before:---
Program gmx, VERSION 5.0.1Source code file:
/home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311
Fatal error:Topology include file gb.itp not foundFor more information and
tips for troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors---
This means someone has removed gb.itp from the charmm36.ff directory and hence
grompp fails. If someone has been toying with the contents of the force field,
start fresh with a new tarball from
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs.
-Justin
Line 311 is the contents of this if statement
if (!cpp-fn){gmx_fatal(FARGS, Topology include file \%s\ not
found, filenm);}
Sincerely,Thomas
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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] Error while shrinking lipids (KALP15 in DPPC tutorial)
Dear gmx-users,
I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the
CHARMM36 forcefield. I think the lipid shrinking was a step I did badly last
time (I think I was getting can open em.tpr but not open em1.tpr, em2.tpr,
etc.), which might be why that run had poor lipid packing.
This is the page of the tutorial I am stuck
at:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The KALP15 in DPPC tutorial says to scale down the lipids by 0.95 for 26 times.
So I repeated this group of 3 commands 26 times:/usr/local/gromacs/bin/gmx
grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o
em.tpr/usr/local/gromacs/bin/gmx mdrun -s em.tpr -vperl inflategro.pl
confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
I am not sure what file to check to make sure doing that is right. I hope it
is.
Anyway I also tried:
cp em.tpr em1.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p
topol.top -o em1.tpr/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -vperl
inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5
area_shrink2.datcp em1.tpr em2.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p
topol.top -o em2.tpr/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -vperl
inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5
area_shrink3.datcp em2.tpr em3.tpr
etc.
But then I got this error I have never seen
before:---
Program gmx, VERSION 5.0.1Source code file:
/home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311
Fatal error:Topology include file gb.itp not foundFor more information and
tips for troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors---
Line 311 is the contents of this if statement
if (!cpp-fn) { gmx_fatal(FARGS, Topology include file \%s\
not found, filenm); }
Sincerely,Thomas
--
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.
