[gmx-users] Charge fitting
Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) I have red a paper ( Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies Justin A. Lemkul, William J. Allen, and David R. Bevan*) about this issue. In this paper they assign these value to each atom: H3C 0.000 CH2 0.150 O-0.548 H 0.398 My question is: In a gromos 43a1 force field and in .rtp file for CH3 in ALA and TMP: [ ALA ] [ atoms ] N N-0.28000 0 H H 0.28000 0 * CA CH1 0.0 1 CB CH3 0.0 1* C C 0.380 2 O O -0.380 2 [ TMP ] [ atoms ] N1NR-0.36000 0 C2 C 0.36000 0 NA2NT-0.83000 1 . . . * CM13 CH3 0.18000 6* C15 C 0.18000 7 O15OA-0.36000 7 * CM15 CH3 0.18000 7* C14 C 0.18000 8 O14OA-0.36000 8 * CM14 CH3 0.18000 8* and for atom O I have same problem: [ ADE ] [ atoms ] P P 0.99000 0 O1POM-0.63500 0 O2POM-0.63500 0 * O5*OA-0.36000 0* C5* CH2 0.0 1. . . * O2*OA-0.54800 8* H2* H 0.39800 8 C3* CH1 0.000 9 * O3*OA -0.36010* So I am confused which one of these charges must be considered as a correct charge when I dont have a reference like mentioned paper? Thanks in advance. P.Haghighi -- 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] Charge fitting
On 2012-01-01 10:11, parto haghighi wrote: Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) Check this paper for gromos96 compatible stuff: http://pubs.acs.org/doi/abs/10.1021/ct200196m For OPLS/GAFF please check http://virtualchemistry.org/ I have red a paper ( Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies Justin A. Lemkul, William J. Allen, and David R. Bevan*) about this issue. In this paper they assign these value to each atom: H3C 0.000 CH2 0.150 O-0.548 H 0.398 My question is: In a gromos 43a1 force field and in .rtp file for CH3 in ALA and TMP: [ ALA ] [ atoms ] N N-0.28000 0 H H 0.28000 0 _*CA CH1 0.0 1 CB CH3 0.0 1*_ C C 0.380 2 O O -0.380 2 [ TMP ] [ atoms ] N1NR-0.36000 0 C2 C 0.36000 0 NA2NT-0.83000 1 . . . _* CM13 CH3 0.18000 6*_ C15 C 0.18000 7 O15OA-0.36000 7 *_ CM15 CH3 0.18000 7_* C14 C 0.18000 8 O14OA-0.36000 8 *_ CM14 CH3 0.18000 8_* and for atom O I have same problem: [ ADE ] [ atoms ] P P 0.99000 0 O1POM-0.63500 0 O2POM-0.63500 0 *_O5*OA-0.36000 0_* C5* CH2 0.0 1. . . *_O2*OA-0.54800 8_* H2* H 0.39800 8 C3* CH1 0.000 9 *_O3*OA -0.36010_* So I am confused which one of these charges must be considered as a correct charge when I dont have a reference like mentioned paper? Thanks in advance. P.Haghighi -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Fw: The results of your email commands
Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging oxygen atoms) I think what it means is that Na+ was added in a distance of 6 Å from the phosphorus. How can we specify this in GROMACS? there is no such option in genion tool in gromacs package. Thank you B.Mehrazma---BeginMessage--- Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging oxygen atoms) I think what it means is that Na+ was added in a distance of 6 Å from the phosphorus. How can we specify this in GROMACS? there is no such option in genion tool in gromacs package. Thank you B.Mehrazma---End Message--- -- 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] Segmentation fault
Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) saba@linuxserver:~/complex/MD I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? I urgently need to study secondary structure during simulations Thanks... -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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] Segmentation fault
On 2/01/2012 12:35 AM, Saba Ferdous wrote: Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) saba@linuxserver:~/complex/MD I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? Assuming other GROMACS tools work, you've done something wrong with the DSSP installation, but it's impossible for us to say what. Note that the version of DSSP released on the last year or two is unsuitable - get the old one. Mark -- 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] grompp error for CNT+surfactant simulation
Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950 12.011 1C 0.142 Copls_9960 12.011 2C 0.142 C 0.142 Copls_9970 12.011 3C 0.142 C 0.142 C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 3.I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 4.I added these to ffnonbonded.itp opls_995 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_996 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_997 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_998 C 612.01100 0.000 A3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for DTAB #include DTAB.itp ; Include topology for CNT #include cnt.itp ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include oplsaa.ff/spc.itp 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.03e+00 There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1356 Fatal error: There were 9 errors in input file(s) --- I would be more than pleased if someone could guild me how to solve the problem. -- 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] After installation help
Hey Mark, thanks for your help. It was extremely useful, now it's solved and running XD. Nice year friend :) Willian Felix On Sat, Dec 31, 2011 at 10:36 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 31/12/2011 11:58 PM, Willian Pereira Felix wrote: Hello buddies, I'm a very beginner in gromacs and I just got a trick but simple situation (for you :D). After the installation of my gromacs on ubuntu 11.10 I opened the .bashrc file and put the following code in the following place as instructed by installation session on the webpage: .BASHRC file # Add an alert alias for long running commands. Use like so: # sleep 10; alert alias alert='notify-send --urgency=low -i $([ $? = 0 ] echo terminal || echo error) $(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;|]\s*alert$//'\'')' # Alias definitions. # You may want to put all your additions into a separate file like # ~/.bash_aliases, instead of adding them here directly. # See /usr/share/doc/bash-doc/examples in the bash-doc package. if [ -f ~/.bash_aliases ]; then . ~/.bash_aliases fi #this should be an access to gromacs source . /usr/local/gromacs/bin/GMXRC source and dot are synonyms... use only one, as instructed here: http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation. This includes the contents of that file into the rc file, and propagates the changes to the calling shell. Mark # enable programmable completion features (you don't need to enable # this, if it's already enabled in /etc/bash.bashrc and /etc/profile # sources /etc/bash.bashrc). if [ -f /etc/bash_completion ] ! shopt -oq posix; then . /etc/bash_completion fi I already tried using . /usr/local/gromacs/GMXRC in the begin and also just /usr/local/gromacs/GMXRC (without the point) and even thereafter I couldn't run the program. Unfortunately I really don't know what to do I've already read the final installation instructions many times and tried to google something related but I had no luck. Please someone can provide me some light on this issue?? Thanks all of you. Willian Felix -- 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] grompp error for CNT+surfactant simulation
niaz poorgholami wrote: Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950 12.011 1C 0.142 Copls_9960 12.011 2C 0.142 C 0.142 Copls_9970 12.011 3C 0.142 C 0.142 C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 3.I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 4.I added these to ffnonbonded.itp opls_995 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_996 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_997 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_998 C 612.01100 0.000 A3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for DTAB #include DTAB.itp ; Include topology for CNT #include cnt.itp ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include oplsaa.ff/spc.itp 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 So here grompp finds that you're overriding default force field parameters by using some customized bond types. This may or may not be what you want/need, so check carefully. If these are indeed what you are after, then there is no problem here. Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types To solve this error and the subsequent ones, check your topology at the quoted line, identify which atom types the interaction pertains to, and determine which parameters need to be added to ffbonded.itp. The no default types error comes from the situation in which grompp cannot assign any parameters to the listed interaction. ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.03e+00 The fractional net charge here indicates that at least one of the topologies (.itp) is broken such that you get a nonsensical sum of charges. It needs to be an integer. -Justin -- 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
