[gmx-users] energy minimisation error
Dear All, Good morning. I am doing the Protein Ligand complex simulation tutorial from the Gromacs website. I followed the tutorial without any issue. When I want to run the energy minimisation md, i get the error message Fatal error: grid cell cx -2147483648 cy -2147483648 out of range (max 24 24) atom -nan -nan -nan, grid->c0 0.00 0.00 I suppose the system is blowing up. There is another error in the nohup file WARNING: Listed nonbonded interaction between particles 2615 and 2632 at distance 3.841 which is larger than the table limit 2.470 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Not sure which parameter to change How to resolve the error? I have Gromacs 2019.4 on an ASUS TUF laptop with AMD Ryzen processor. Thank you Regards -- 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] water deletor script error
Dear All, I used Dr. Justin's perl script to delete water from the membrane. It gives an error of illegal division by zero. has anyone experienced it. i looked at the error line it goes like this my $middle_z = $total_z / $nmiddle; I tried a few atom numbers but same error. i wonder if others had som eerror Thanks -- 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] warnings about tip3
Dear All, I m simulating cholesterol membrane with protein embedded in water portion of the upper leaflet of the membrane. I am using Gromacs 2019 built on Windows 10 WSL. My intention is to pull the protein through the membrane from one end to the other into the water part. The membrane was built on CHARMM-GUI and it added the TIP3 water molecules on both sides of the membrane. Using Charmm36 in Gromacs, i prepared the protein without error. I was able to add ions and solvate the system without any issue. Now when I want to minimise it , i am getting warnings when running the grompp to generate the tpr that I would like to understand. I looked on the internet and as per advice looked the TIP3.itp. the warning is: WARNING 1 [file TIP3.itp, line 25]: Too few parameters on line (source file /mnt/e/gromacs/gromacs-2019/src/gromacs/gmxpreprocess/toppush.cpp, line 1326) And line 25 is ;[ settles ] ; i j funct length 1 1 9.572000e-02 1.513900e-01 Also the note below says NOTE 2 [file topol.top, line 1394]: In moleculetype 'TIP3' 3 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. I checked line mentioned . given in red [ molecules ] ; Compound#mols Protein_chain_a 1 CHL1256 TIP3 7171 SOL 67764 CL 1 Any idea how to correct the error? should i have changed the TIP3 to SOL before solvating. thank you -- 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] various issues when simulating cholesterol membrane
Dear All, It has been a futile effort so far when I want to just simulate a simple cholesterol membrane. I checked the mailing list. but some how my issues was not really answered. So after following a few answers and solutions here and there, i would like to as a few questions which i cannot solve even after following the solutions posted. 1. My cholesterol membrane was prepared usingthe CHARMM Membrane BUilder, hence it sed the xharmm forcefield. There is only 1 charmm forcefield in Gromacs 2019 Charmm27. so, I downloaded the forcefield and parameter files Slipids_2016 from the http://www.fos.su.se/~sasha/SLipids/. I used the non bonded and bonded forcefield parameters given as there is a unique hydrogen named H3' which is not found in other forcefields such as Gromos53A6 or 54A7. Although when I used 54A7 parameterised cholesterol.itp from ATB server, i got the error or naming mismatch which i thinks is because the number of cholesterol atoms in the ATB file is only 31 while my pdb file has 74 atoms per molecule and also the atom types are different. If I use the normal charmm27 forcefield extended to BERGER lipids, error of proper dihedrals, U-B atoms and i j parameters comes when it reads the cholesterol.itp. So when i will want to parametrise the protein, i will have issues or can i use the same forcefield since the file does have the amino acid parameters also? Kindly suggest what can be the correct way? Thank you Regards Ayesha Fatima -- 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] CHOL still not recognised
Dear Justin, Thank you for your earlier response. I opened the file in vmd and it returned me with a 3 letter residue name and an X identifier for the whole molecule. CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 C3 CHL X 1 -1.678 2.702 17.328 1.00 0.00 MEMB C ATOM 2 H3 CHL X 1 -0.722 3.268 17.289 1.00 0.00 MEMB H ATOM 3 O3 CHL X 1 -2.187 2.686 18.672 1.00 0.00 MEMB O ATOM 4 H3' CHL X 1 -1.369 2.855 19.145 1.00 0.00 MEMB H .. ATOM 9473 OH2 TIP X 1 0.049 2.793 20.554 1.00 0.00 TIP3 O ATOM 9474 H1 TIP X 1 0.881 2.777 20.081 1.00 0.00 TIP3 H ATOM 9475 H2 TIP X 1 0.235 2.351 21.383 1.00 0.00 TIP3 H ATOM 9476 OH2 TIP X 2 -1.458 -2.368 19.953 1.00 0.00 TIP3 O ATOM 9477 H1 TIP X 2 -2.185 -2.795 20.406 1.00 0.00 TIP3 H now when i run pdb2gmx, the error is Fatal error: The residues in the chain CHL1--TIP3130 do not have a consistent type. The first residue has type 'Other', while residue TIP1 is of type 'Water'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it's a separate molecule. i cant find the solution to the error online. would you or anyone one the list guide? Thank you regards -- 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] gromacs is not recognising opls ff
Dear All, I have come across another issue When i want to use opls itp for cholesterol, it gives me this error " Fatal error: Residue 'OL' not found in residue topology database" It does not take CHOL as the residue name as given below [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_158 1 CHOL C1 1 0.2050 12.011 2 opls_140 1 CHOL H1 1 0.0600 1.008 3 opls_154 1 CHOL O1 1 -0.6830 15.9994 Any suggestions? Thank you regards -- 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] gromacs.org_gmx-users Digest, Vol 180, Issue 46
Thank you Rahul for the response. I tried that but still cant see it. In addition to my previous question,. how do we restrain the lipid membrane in one direction only. I came across the GROMACS documentation where it sytes the freedim parameter. Is it placed in the pull md parameter file of elsewhere? Thank you On Sun, Apr 14, 2019 at 1:53 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: Problem regarding grompp command (Encountered a second > block of parameters for dihedral type 9 for the same atoms...) > (RAHUL SURESH) >2. Re: Problem regarding grompp command (Encountered a second > block of parameters for dihedral type 9 for the same atoms...) > (RAHUL SURESH) >3. make index for protein multiple ligand md simulation (m mar) >4. Re: make index for protein multiple ligand md simulation > (Soham Sarkar) >5. GMO simulation (Ayesha Fatima) >6. Re: GMO simulation (RAHUL SURESH) > > > -- > > Message: 1 > Date: Sun, 14 Apr 2019 00:50:10 +0530 > From: RAHUL SURESH > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Problem regarding grompp command (Encountered > a second block of parameters for dihedral type 9 for the same > atoms...) > Message-ID: > < > caatfitssehgq-cuqkfejas0p9f1rwxfbpkwabftbhzrrads...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi > > You have messed different versions of prm and charmm file. Please have a > check with the charmm generated prm and FF files. > > Thank you > > > On Thu 4 Apr, 2019, 7:05 PM Chem, wrote: > > > To > > Prof. Justin A. Lemkul Users > > Dear Gromacs users > > > > I am learning MD simulation of protein-ligand interaction using an > > important Gromacs software, applied to my compound; 3b-Acetoxy-6-nitro > > cholest-5-ene.When I implemented the commands given below. I faced the > > problem.I read many questions and answers related to my problem, but I > > could not find the appropriate answer. > > > > $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > ERROR 11 [file unk.prm, line 264]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > ERROR 12 [file unk.prm, line 265]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > Line 264 CG3C52 CG3C52 CG3RC1CG311 9 > > 0.00 0.418400 3 > > > > Line 265 CG3C52 CG3C52 CG3RC1CG311 9 > > 0.00 2.092000 4 > > > > . > > > > . > > > > > > > > > > > > > ... > > > > I need your kind help to overcome this problem, so I learn the simulation > > smoothly > > > > I look forward to your useful help with the above problem > > > > Please suggest me what I should do > > > > > > > > > > Regards > > M. Alam > > > > -- > > 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] GMO simulation
Dear All, I have a glyceryl monooleate 100 molecule assembly. I want to pull a peptide like molecule through it. I have obtained the forcefield files from *Boeckmann, Rainer website.* I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but got stuck as the force field obtained from Rainer website and put in the working directory, the path to working directory does not appear in the list of forcefields. i prepared my molecule using 54a7 forcefield implemented in ATB server. i got the itp files and prepared the gro file using editconf My question is to anyone who has done the glycerol simulation using gromacs. please help with the exact procedure to develop the simulation files. Should I add the 54a7 forcefield with to the OPLSAA updated forcefield by Prof Rainer or vice versa? I also have a peptide like molecule to pull through the GMO membrane. Any one can help guide through this? Thank you in anticipation Ayesha -- 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] Pull code errors
Dear All, I am using Gromax 2019 and running an umbrella sampling for two proteins. It is a simple pulling simulation. It is giving me the following error ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a specific atom selected as reference atom. ERROR 2 [file md_pull.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 2 is larger than that and does not have a specific atom selected as reference atom. Pull group natoms pbc atom distance at start reference at t=0 1 9157 4579 2 589 5113 0.300 nm 0.300 nm Estimate for the relative computational load of the PME mesh part: 0.14 -- Is there anything to be added in the pull code? Thank you Regards -- 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] gromacs compilation in cygwin
Dear All, I am trying to install gromacs 5.0.5 in cygwin. I am getting linking errors to fftw. although i have added the path in my bashrc file. can someone help . the errors: ../libtool: line 6002: cd: home/ashmer/fftw-3.3.4/fftw-3.3.4/lib: No such file or directory libtool: link: cannot determine absolute directory name of `home/ashmer/fftw-3.3.4/fftw-3.3.4/lib' Makefile:308: recipe for target 'libkernel.la' failed make[5]: *** [libkernel.la] Error 1 Makefile:548: recipe for target 'all-recursive' failed make[4]: *** [all-recursive] Error 1 Makefile:416: recipe for target 'all' failed make[3]: *** [all] Error 2 src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:110: recipe for target 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-build' failed make[2]: *** [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-build] Error 2 CMakeFiles/Makefile2:1082: recipe for target 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2 Makefile:147: recipe for target 'all' failed make: *** [all] Error 2 ... in the bashrc file export PATH=$PATH:/home/ashmer/fftw-3.3.4/fftw-3.3.4 export CPPFLAGS=-I$/home/ashmer/fftw-3.3.4/fftw-3.3.4/include export LDFLAGS=-L$/home/ashmer/fftw-3.3.4/fftw-3.3.4/lib export Gromacs5=/cygdrive/c export PATH=$Gromacs5/bin:$PATH export LD_LIBRARY_PATH=$Gromacs5/lib:$LD_LIBRARY_PATH ... thank you Ayesha Fatima (UM) -- 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] calculating distances in steered dynamics
Dear Gromacs Users, I recently started using gromacs 5.0.4 for SD. I modified a few things here and there as per changes in gromacs 5.0.4. The SD ran fine. Now I want to calculate the distances from the conf0.gro file as per Justin's tutorial. I want to use the distance.pl file but i am not sure of the changes I am attaching the file with the changes I did. but it is giving me error Use of uninitialized value $distance in concatenation (.) or string at distances.pl line 30. this is the line for printing out the distances. How to modify for gromacs 5.0.4? BTW, Thank you Justin for the advice. I will follow after I complete this run. Thank you Regards Ayesha Fatima PhD candidate (UM) -- 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 in umbrella sampling tutorial
Dear Justin, I am learning to use the steered dynamics method implemented in gromacs. somehow your website is not accessible today so i cannot download the modified files of the fibrils for simulation. so i started withe the original file 2BEG.pdb and if i dont select the N and C termini modifications i get the error ... There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. . Could you guide me through the issue? Thank you Regards Ayesha Fatima PhD candidate, UM, Malaysia -- 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] testing gromacs runs
Dear all, I have just installed gromacs 4.6.5 in Cygwin build on Windows 7 platform. I want to test the installation but it keeps giving the error ./gmxtest.pl all ERROR: Can not find executable gmx pdb2gmx in your path. Please source GMXRC and try again. My Gromacs is installed in the C: drive outside the root. I have also put the regression folder downloaded from http://gerrit.gromacs.org/download/regressiontests-4.6.5.tar.gz I sourced gromacs from inside the folder where the file gmxtest.pl is. However when i want execute pdb2gmx, the file executes Could you guide please? thank you Ayesha -- 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.
