[gmx-users] proper dihedral types in the topology
Dear man or madam, I have a question about the dihedral types in the topology. If I made the topology by hand, is it possible to combine the type 9 and type 3 for proper dihedrals? Any comment about that? Thanks. Best, Lu -- 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] termini modification
Hello, I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here is my code for the aminoacids.c.tdb [ COO- ] [ replace ] HH1.008000.27190 NN14.01000-0.41570 CACT12.010000.03370 HAH11.008000.08230 CC12.010000.59730 CBCT12.01-0.1825 HB1HC1.0080.0603 HB2HC1.0080.0603 HB3HC1.0080.0603 [ add ] 11OCCAN O16.0-0.56790 [ bonds ] CO 10.12290476976.0 [ delete ] OC1 OC2 when I run pdb2gmx using this termini modification, everything works fine except the deletion of OC1 and OC2 atoms, the error which I get for this run as follows, Fatal error: Atom OC2 not found in residue seq.nr. 8 while adding atom any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ delete ] option with the aminoacids.c.tdb file, it works fine by adding the O atom to the terminal residue including the presence of OC1 and OC2 atoms. first I am trying to modify the c terminal residue. Regards, vijay. -- 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] termini modification
pdb2gmx -ter On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj wrote: > Hello, > > I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the > terminal residues from NALA and CALA to normal ALA (just as middle > residues). As the terminal selection option is not enabled with the amber > ff, I am using the termini modification parameters with aminoacids.c.tdb. > here is my code for the aminoacids.c.tdb > > [ COO- ] > > [ replace ] > H H 1.00800 0.27190 > N N 14.01000 -0.41570 > CA CT 12.01000 0.03370 > HA H1 1.00800 0.08230 > C C 12.01000 0.59730 > CB CT 12.01 -0.1825 > HB1 HC 1.008 0.0603 > HB2 HC 1.008 0.0603 > HB3 HC 1.008 0.0603 > > [ add ] > 1 1 O C CA N > O 16.0 -0.56790 > > [ bonds ] > C O 1 0.12290 476976.0 > > [ delete ] > OC1 > OC2 > > > when I run pdb2gmx using this termini modification, everything works fine > except the deletion of OC1 and OC2 atoms, the error which I get for this run > as follows, > > Fatal error: > Atom OC2 not found in residue seq.nr. 8 while adding atom > > > any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ > delete ] option with the aminoacids.c.tdb file, it works fine by adding the > O atom to the terminal residue including the presence of OC1 and OC2 atoms. > first I am trying to modify the c terminal residue. > > Regards, > vijay. > > -- > gmx-users mailing list gmx-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 > -- Best Regards, lina -- 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] termini modification
lina wrote: pdb2gmx -ter I doubt this is of any use; the Amber force fields don't use the same conventional termini selection that the other force fields do, as the OP states. I suspect that's why the .tdb approach is not working. I think the best approach is to simply write .rtp entries for the modified terminal residues with unique names such that they are distinguished from all other residues. I don't know if it will work (since termini in Amber are treated differently), but it's worth a try. -Justin On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj wrote: Hello, I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here is my code for the aminoacids.c.tdb [ COO- ] [ replace ] HH1.008000.27190 NN14.01000-0.41570 CACT12.010000.03370 HAH11.008000.08230 CC12.010000.59730 CBCT12.01-0.1825 HB1HC1.0080.0603 HB2HC1.0080.0603 HB3HC1.0080.0603 [ add ] 11OCCAN O16.0-0.56790 [ bonds ] CO 10.12290476976.0 [ delete ] OC1 OC2 when I run pdb2gmx using this termini modification, everything works fine except the deletion of OC1 and OC2 atoms, the error which I get for this run as follows, Fatal error: Atom OC2 not found in residue seq.nr. 8 while adding atom any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ delete ] option with the aminoacids.c.tdb file, it works fine by adding the O atom to the terminal residue including the presence of OC1 and OC2 atoms. first I am trying to modify the c terminal residue. Regards, vijay. -- 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 -- 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 -- 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] cannot inactivate fitting in g_rmsf - incomplete coordinates are written
Dear GROMACS community, I am trying to calculate B-factors of a sample equilibrated system (31 frames). My trajectory is in .psf and .dcd format but I have created a .tpr file for my analysis from the first frame . First I eliminated random translation and rotation of my protein by fitting every frame to the first one (I selected to fit CA atoms and write the whole system back): trjconv -f truncated_WT.dcd -o truncated_WT_fitted.trr -s truncated_initial_WT.tpr -fit rot+trans Then I tried to calculate the average coordinates and save then in a .pdb file, either by first fitting all the frames to the first one (I selected to fit CA atoms): g_rmsf -f truncated_WT_fitted.trr -s truncated_initial_WT.tpr -ox -fit or without doing a least squares superposition (I selected to fit CA atoms - bizarre) : g_rmsf -f truncated_WT_fitted.trr -s truncated_initial_WT.tpr -ox -nofit However, in the latter case I am always prompted to select group(s) for root mean square calculation, and besides that the average coordinates written to the xaver.pdb file are incomplete. These are the first 10 lines: ==> xaver_fit_grmsf.pdb <== TITLE vmdmolecule0 REMARKTHIS IS A SIMULATION BOX CRYST1 125.654 115.248 133.144 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 5 CA MET 1 98.823 64.559 100.152 1.00408.90 ATOM 24 CA PRO 2 98.801 61.706 101.694 1.00232.79 ATOM 38 CA PRO 3 96.250 62.337 103.868 1.00106.03 ATOM 50 CA ARG 4 92.760 61.521 102.890 1.00 69.93 ATOM 76 CA PRO 5 89.888 63.926 103.105 1.00 71.21 ATOM 88 CA SER 6 88.220 63.301 106.384 1.00 41.38 ==> xaver_nofit_grmsf.pdb <== TITLE vmdmolecule0 REMARKTHIS IS A SIMULATION BOX CRYST1 125.654 115.248 133.144 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 5 CA MET 1 98.819-nan 100.135 1.00407.71 ATOM 24 CA PRO 2 98.801-nan 101.677 1.00231.97 ATOM 38 CA PRO 3 96.249-nan 103.853 1.00105.71 ATOM 50 CA ARG 4 92.760-nan 102.876 1.00 69.63 ATOM 76 CA PRO 5 89.886-nan 103.092 1.00 70.84 ATOM 88 CA SER 6 88.220-nan 106.373 1.00 41.21 The same happens no matter what group I select for fitting and or which version of GROMACS Tools I use (4.5.4, 4.0.5). I also tried to use .xtc and .pdb file formats instead of .trr and .trp without any luck. Surprisingly I could get complete coordinates from g_covar v4.5.4 without fitting, without being prompted to choose a group for the least squares fit. However, g_covar is much slower than g_rmsf and I would avoid using it for the whole trajectory if I could. For the sake of comparison these are the average coordinates I got from g_covar with and without fitting (file names are self-explanatory): ==> average_fit_gcovar.pdb <== TITLE Average structure MODEL1 ATOM 5 CA MET 1 31.396 3.841 9.383 1.00 0.00 ATOM 24 CA PRO 2 31.375 0.988 10.924 1.00 0.00 ATOM 38 CA PRO 3 28.823 1.620 13.099 1.00 0.00 ATOM 50 CA ARG 4 25.334 0.802 12.120 1.00 0.00 ATOM 76 CA PRO 5 22.461 3.208 12.336 1.00 0.00 ATOM 88 CA SER 6 20.794 2.581 15.615 1.00 0.00 ATOM 99 CA SER 7 19.269 4.709 18.340 1.00 0.00 ATOM110 CA GLY 8 21.111 5.337 21.583 1.00 0.00 ==> average_nofit_gcovar.pdb <== TITLE Average structure MODEL1 ATOM 5 CA MET 1 98.815 64.568 100.152 1.00 0.00 ATOM 24 CA PRO 2 98.794 61.715 101.694 1.00 0.00 ATOM 38 CA PRO 3 96.243 62.347 103.869 1.00 0.00 ATOM 50 CA ARG 4 92.753 61.529 102.890 1.00 0.00 ATOM 76 CA PRO 5 89.880 63.935 103.105 1.00 0.00 ATOM 88 CA SER 6 88.213 63.308 106.385 1.00 0.00 ATOM 99 CA SER 7 86.688 65.436 109.109 1.00 0.00 ATOM110 CA GLY 8 88.530 66.064 112.353 1.00 0.00 I also visualized truncated_WT_fitted.trr and average_nofit_gcovar.pdb in VMD and concluded that the average coordinates of average_nofit_gcovar.pdb are most likely correct (you can also work it out by comparing the coordinates of average_nofit_gcovar.pdb, xaver_fit_grmsf.pdb and xaver_nofit_grmsf.pdb). Any ideas what I am doing wrong with g_rmsf? thanks in advance, Thomas -- 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] part number in extending simulation
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt 12 \
-s ${a}/md100ns.tpr \
-o ${a}/md100ns.trr \
-e ${a}/md100ns.edr \
-g ${a}/md100ns.log \
-c ${a}/md100ns.gro \
-cpo ${a}/md100ns.cpt \
-cpi ${a}/md50ns.cpt
#
In GROMACS ver.4.0.5, if I use this script I'll get files such as
md100ns.part002.trr,
md100ns.part002.gro, md100ns.part002.edr, and md100ns.part002.log.
But in ver.4.5.4 I only get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hsin-Lin
--
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
