Re: [gmx-users] OWT5 not found in Charmmff
- Original Message - From: Yao Yao ya...@ymail.com Date: Saturday, September 11, 2010 10:00 Subject: [gmx-users] OWT5 not found in Charmmff To: gmx-users@gromacs.org I am running tip5p in charmm force field in gmx. In energy minimization step, it gives an error msg as below. I just simply added it in atomtypes.atp in charmm27.ff, but still it doesn't work. Does anyone know how to solve it? Depends what you've done. My instructions about copying the charmm27.ff directory should have worked. More than tip5p.itp is required, and it has to go where pdb2gmx will find it - either in the local copy of the directory, or in the $GMXLIB version.. Mark --- Program grompp, VERSION 4.5-beta3 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT5 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- -- 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] please help, cannot compile gmx 4.5 openmm
Hi Alan, I assume this is still the same issue on the same issue (same machine/os) as you reported last time. Could you provide some details about the version of OS, compiler, CUDA, OpenMM you're using? I'll look into the problem and get back to you if I figure out something. Cheers, -- Szilárd On Sat, Sep 11, 2010 at 12:56 AM, Alan alanwil...@gmail.com wrote: I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing list gmx-us...@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] Problem Installing 4.5.1
OpenSuSE 11.2 on 64bit AMD computer. Compiling and installation went smoothly without any warning or error messages. However, when I attempted running gmxdemo, the execution hund in pdb2gmx, the output file is attached. Any help will be much appreciated. Thanks in advance. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivarate http://www.FoundationForChemistry.com output.pdb2gmx Description: Binary data -- 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] Problem Installing 4.5.1
On 2010-09-12 16.17, Stephen P. Molnar wrote: OpenSuSE 11.2 on 64bit AMD computer. Compiling and installation went smoothly without any warning or error messages. However, when I attempted running gmxdemo, the execution hund in pdb2gmx, the output file is attached. Any help will be much appreciated. Thanks in advance. There is an error in the demo script. Please move on to the next part of the tutorial. We'll fix it for the next point release. -- 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] charmm to gromacs nonbonded parameters after conversion
Hi GMX users, I would like to perform MD with new developped CHARMM parameters in GROMACS. Since these parameters are new, they are not presents in the ffcharm*.itp files given in the of charmm27.ff in the latest GMX distribution. So I have already made the conversions for the bonded parameters. In case of the nonbonded parameters, I have added the LJ values for the new atom types at the end of the NONBONDED section of a par_all_27_lipid.prm file downloaded from the CHARMM website. To convert the LJ values in GROMACS format, I used the perl script of M. Abraham : convert_charmm_to_gromacs.pl (v.1.3) as follow : perl convert_charmm_to_gromacs.pl par_all27_lipid.prm I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected. In the ffcharmmnb.itp the [ atomtypes ] section is present but not the [ pairtypes ] section. Moreover the values in the [ atomtypes ] are different compared to same file given in latest GMX distrib (see below). Why these differences ? - My ffcharmmnb.itp file [ atomtypes ] ;name mass charge ptype c6 c12 CTL1 12.011000 0.0 A -0.001485 -6.588e-06 ; -0.000252 -3.793e-07 CTL2 12.011000 0.0 A -0.001978 -4.173e-06 ; -0.000252 -3.793e-07 CTL3 12.011000 0.0 A -0.003011 -6.944e-06 ; -0.000252 -3.793e-07 CTL5 12.011000 0.0 A -0.003274 -8.007e-06 ; -0.000252 -3.793e-07 CEL1 12.011000 0.0 A -0.003035 -8.095e-06 -- GROMACS 4.5.1 ffcharmmnb.itp [ atomtypes ] ;name at.num mass charge ptype sigma epsilon CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 CTL2 6 12.01100 0.05 A 0.358141284692 0.234304 CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472 CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 . Thank in advance for your halp Stefane -- 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] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?
Dear all, I have two question: 1) Are the atom types I chose for the use of OPLS force field correct? I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg Server converts PDB files of drug structures just in an .itp file compatible with gromos forcefields, I had to change the atom types as follows: drug.itp: [ moleculetype ] ; Name nrexcl drug 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1opls_145 1 DRG C1 1 -0.018 13.0190 2opls_729 1 DRG C2 10.002 12.0110 3opls_730 1 DRGBR1 10.016 79.9040 4opls_166 1 DRG C3 20.149 12.0110 5opls_167 1 DRG O1 2 -0.174 15.9994 6opls_168 1 DRGHAA 20.066 1.0080 7opls_145 1 DRG C4 2 -0.020 13.0190 8opls_145 1 DRG C5 2 -0.021 13.0190 9opls_145 1 DRG C6 30.002 12.0110 10 opls_136 1 DRG C7 30.093 14.0270 11 opls_139 1 DRG C8 30.172 12.0110 12 opls_750 1 DRG N1 3 -0.267 14.0067 13opls_154 1 DRG O2 4 -0.108 15.9994 14opls_155 1 DRGHAB 40.108 1.0080 15 opls_235 1 DRG C9 50.395 12.0110 16 opls_236 1 DRG O3 5 -0.664 15.9994 17 opls_237 1 DRG N2 50.159 14.0067 18 opls_240 1 DRGHAD 50.024 1.0080 19 opls_136 1 DRGC10 50.086 14.0270 20 opls_206 1 DRGC11 60.000 14.0270 21 opls_083 1 DRG S1 7 -1.000 32.0600 Drug.gro: PRODRG COORDS 21 1DRG C1 1 8.555 5.270 -3.838 1DRG C2 2 8.529 5.317 -3.967 1DRG BR1 3 8.392 5.231 -4.068 1DRG C3 4 8.602 5.424 -4.019 1DRG O1 5 8.580 5.472 -4.145 1DRG HAA 6 8.507 5.419 -4.189 1DRG C4 7 8.700 5.485 -3.941 1DRG C5 8 8.725 5.438 -3.812 1DRG C6 9 8.653 5.331 -3.760 1DRG C7 10 8.681 5.281 -3.619 1DRG C8 11 8.788 5.172 -3.616 1DRG N1 12 8.913 5.205 -3.598 1DRG O2 13 8.945 5.341 -3.583 1DRG HAB 14 9.044 5.351 -3.570 1DRG C9 15 8.736 5.032 -3.632 1DRG O3 16 8.619 5.004 -3.652 1DRG N2 17 8.828 4.932 -3.624 1DRG HAD 18 8.925 4.956 -3.626 1DRG C10 19 8.790 4.792 -3.610 1DRG C11 20 8.903 4.690 -3.629 1DRG S1 21 8.838 4.520 -3.654 1.11480 1.11480 1.11480 2) Visualization problem of VMD? The second question is related to the first one: I use VMD 1.8.7 under Windows XP. When I try to visualize above mentioned Drg.gro file using VMD, the bromo atom appears as a tiny point and is not connected to C2 as it should. When I convert the Drg.gro file to a pdf-file by the command editconf, the pdf-structure displays the bromo atom correctly connected to the aromatic ring. In addition, during the course of an mdrun over 1 ns the relative position and the distance of the bromo atom to C2 remained unchanged. The distance between BR1 and C2 in the final mdrun after some relaxation was constantly 1.89 Angstrom which is realistic. Is my observation a visualization problem of VMD or a serious problem with gromacs which I do not see. If it is a problem with VMD, Is there a remedy for the incorrect visualization of the drug molecule? Thank you in advance, Franz F.-J. Meyer-Almes Hochschule Darmstadt Fachbereich Chemie- und Biotechnologie Schnittspahnstr. 12 64287 Darmstadt Email: franz-josef.meyer-al...@h-da.de Tel.: ++49-(0)6151-168406 http://www2.h-da.de/cub/index.php?id=177 -- 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] Visualization problem of bromo atom connected to an aromatic ring due to gromacs or VMD?
Meyer-Almes, Franz-Josef, Prof. Dr. wrote: Dear all, I have two question: 1) Are the atom types I chose for the use of OPLS force field correct? I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme drug interaction. Since the Dundee Prodrg Server converts PDB files of drug structures just in an .itp file compatible with gromos forcefields, I had to change the atom types as follows: Simply changing the atom types is not likely an appropriate solution. OPLS-AA is an all-atom force field, in which all H should be represented. You have a grand total of 3 H atoms in this structure. After a quick look at your structure, this is definitely not correct. Also note that the charges that PRODRG generates fall somewhere between marginal and totally incorrect for even the GROMOS force fields. snip 2) Visualization problem of VMD? The second question is related to the first one: I use VMD 1.8.7 under Windows XP. When I try to visualize above mentioned Drg.gro file using VMD, the bromo atom appears as a tiny point and is not connected to C2 as it should. When I convert the Drg.gro file to a pdf-file by the command editconf, the pdf-structure displays the bromo atom correctly connected to the aromatic ring. In addition, during the course of an mdrun over 1 ns the relative position and the distance of the bromo atom to C2 remained unchanged. The distance between BR1 and C2 in the final mdrun after some relaxation was constantly 1.89 Angstrom which is realistic. Is my observation a visualization problem of VMD or a serious problem with gromacs which I do not see. I don't see how the problem is with Gromacs - you say that the output of mdrun is reasonable. If you've defined a bond between two atoms, the bond will be there. The topology is correct, VMD's interpretation of the molecule has no such guarantee. If it is a problem with VMD, Is there a remedy for the incorrect visualization of the drug molecule? VMD guesses where bonds should be based on inter-atomic distances. There may be ways around this effect. Many have been mentioned on this list, so a few minutes of poking around in the archive should turn up some useful information. There may also be some information in the VMD mailing list archive or in the VMD manual. -Justin Thank you in advance, Franz F.-J. Meyer-Almes Hochschule Darmstadt Fachbereich Chemie- und Biotechnologie Schnittspahnstr. 12 64287 Darmstadt Email: franz-josef.meyer-al...@h-da.de Tel.: ++49-(0)6151-168406 http://www2.h-da.de/cub/index.php?id=177 -- 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] Polyglycine PDB file.
I'm new to gmx so I'm just seeing if I'm able to make homoblock polypeptides. I would like to simulate a 5 residue polyglycine. I've used PRODRG to generate the pdb file, however trying to convert the file with pdb2gmx I receive the error: Fatal error: Residue 'Y' not found in residue topology database My pdb file is: ATOM1 O GLY 1 -2.600 -2.350 -0.400 1.00 20.00 O ATOM2 C GLY 1 -2.250 -1.400 0.340 1.00 20.00 C ATOM3 O GLY 1 -1.850 -1.490 1.520 1.00 20.00 O ATOM4 CA GLY 1 -2.330 0.010 -0.240 1.00 20.00 C ATOM5 N GLY 1 -3.620 0.630 0.130 1.00 20.00 N ATOM6 C GLY 2 -3.800 1.640 1.000 1.00 20.00 C ATOM7 O GLY 2 -4.910 2.110 1.230 1.00 20.00 O ATOM8 CA GLY 2 -2.600 2.240 1.730 1.00 20.00 C ATOM9 N GLY 2 -2.160 3.460 1.030 1.00 20.00 N ATOM 10 C GLY 3 -2.510 4.720 1.320 1.00 20.00 C ATOM 11 O GLY 3 -2.050 5.670 0.680 1.00 20.00 O ATOM 12 CA GLY 3 -3.510 4.990 2.460 1.00 20.00 C ATOM 13 N GLY 3 -4.640 5.790 1.950 1.00 20.00 N ATOM 14 C GLY 4 -5.930 5.680 2.300 1.00 20.00 C ATOM 15 O GLY 4 -6.800 6.390 1.810 1.00 20.00 O ATOM 16 CA GLY 4 -6.340 4.640 3.360 1.00 20.00 C ATOM 17 N GLY 4 -6.800 5.360 4.570 1.00 20.00 N ATOM 18 C GLY 5 -7.330 4.810 5.670 1.00 20.00 C ATOM 19 O GLY 5 -7.640 5.500 6.640 1.00 20.00 O ATOM 20 CA GLY 5 -7.550 3.300 5.730 1.00 20.00 C ATOM 21 N GLY 5 -8.990 3.000 5.660 1.00 20.00 N END I'm not sure what I could be doing wrong since I pretty much mimicked the speptide.pdb in the tutor file. Thanks for the help, Joe. -- 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] Polyglycine PDB file.
On 2010-09-12 21.13, C Johnson wrote: I'm new to gmx so I'm just seeing if I'm able to make homoblock polypeptides. I would like to simulate a 5 residue polyglycine. I've used PRODRG to generate the pdb file, however trying to convert the file with pdb2gmx I receive the error: Fatal error: Residue 'Y' not found in residue topology database My pdb file is: ATOM 1 O GLY 1 -2.600 -2.350 -0.400 1.00 20.00 O ATOM 2 C GLY 1 -2.250 -1.400 0.340 1.00 20.00 C ATOM 3 O GLY 1 -1.850 -1.490 1.520 1.00 20.00 O ATOM 4 CA GLY 1 -2.330 0.010 -0.240 1.00 20.00 C ATOM 5 N GLY 1 -3.620 0.630 0.130 1.00 20.00 N ATOM 6 C GLY 2 -3.800 1.640 1.000 1.00 20.00 C ATOM 7 O GLY 2 -4.910 2.110 1.230 1.00 20.00 O ATOM 8 CA GLY 2 -2.600 2.240 1.730 1.00 20.00 C ATOM 9 N GLY 2 -2.160 3.460 1.030 1.00 20.00 N ATOM 10 C GLY 3 -2.510 4.720 1.320 1.00 20.00 C ATOM 11 O GLY 3 -2.050 5.670 0.680 1.00 20.00 O ATOM 12 CA GLY 3 -3.510 4.990 2.460 1.00 20.00 C ATOM 13 N GLY 3 -4.640 5.790 1.950 1.00 20.00 N ATOM 14 C GLY 4 -5.930 5.680 2.300 1.00 20.00 C ATOM 15 O GLY 4 -6.800 6.390 1.810 1.00 20.00 O ATOM 16 CA GLY 4 -6.340 4.640 3.360 1.00 20.00 C ATOM 17 N GLY 4 -6.800 5.360 4.570 1.00 20.00 N ATOM 18 C GLY 5 -7.330 4.810 5.670 1.00 20.00 C ATOM 19 O GLY 5 -7.640 5.500 6.640 1.00 20.00 O ATOM 20 CA GLY 5 -7.550 3.300 5.730 1.00 20.00 C ATOM 21 N GLY 5 -8.990 3.000 5.660 1.00 20.00 N END I'm not sure what I could be doing wrong since I pretty much mimicked the speptide.pdb in the tutor file. Thanks for the help, Joe. I guess your pdb file has been damaged by a text editor (Word?). PDB files are fixed format, you can not add or remove spaces at will. You could try clicking together a peptide in Pymol or so, or drop the prodrg output in Notepad (if you're on Windows). On mac or linux it should be straightforward with text editors. -- 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] PBS script
Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Thanks! -- 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] PBS script
manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- 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
Re: [gmx-users] PBS script
Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- 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 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] PBS script
manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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
Re: [gmx-users] PBS script
Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 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] PBS script
Google given a link to very good site in regard. http://biowulf.nih.gov/apps/gromacs/ On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 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] Re: Polyglycine PDB file.
I guess your pdb file has been damaged by a text editor (Word?). PDB files are fixed format, you can not add or remove spaces at will. You could try clicking together a peptide in Pymol or so, or drop the prodrg output in Notepad (if you're on Windows). On mac or linux it should be straightforward with text editors. I copied the PRODRG PDB into vim, changed HETATM to ATOM and DRG to GLY and renumbered the residues. I really don't understand what I could have done wrong. Can you get the file to convert with pdb2gmx? -- 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] Re: Polyglycine PDB file.
C Johnson wrote: I guess your pdb file has been damaged by a text editor (Word?). PDB files are fixed format, you can not add or remove spaces at will. You could try clicking together a peptide in Pymol or so, or drop the prodrg output in Notepad (if you're on Windows). On mac or linux it should be straightforward with text editors. I copied the PRODRG PDB into vim, changed HETATM to ATOM and DRG to GLY and renumbered the residues. I really don't understand what I could have done wrong. Can you get the file to convert with pdb2gmx? If you simple replace HETATM with ATOM, i.e.: :1,$s/HETATM/ATOM/ you shift all columns left by two characters. This is probably why, instead of reading GLY, pdb2gmx is reading Y only. The proper replacement would be: :1,$s/HETATM/ATOM / Note the two trailing spaces after ATOM. -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
[gmx-users] PBS script
Manoj, to suggest that Justin is being lazy would be to ignore the hundreds, possibly thousands, of helpful posts that he has made on the gromacs mailing list to assist users like yourself free of charge. In fact, Justin was probably helping you more than you have realized by pointing out that you can access some of this information in places other than the gromacs mailing list, and yes, google is one of those places. Chris. -- original message -- Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalemkul at vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -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
Re: [gmx-users] PBS script
it must be hard to do your own research On Sep 12, 2010, at 5:52 PM, manoj singh wrote: Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 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] Re: Re: Polyglycine PDB file.
If you simple replace HETATM with ATOM, i.e.: :1,$s/HETATM/ATOM/ you shift all columns left by two characters. This is probably why, instead of reading GLY, pdb2gmx is reading Y only. The proper replacement would be: :1,$s/HETATM/ATOM / Note the two trailing spaces after ATOM. -Justin Justin, adding the two spaces did the job. Thanks -- 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] charmm to gromacs nonbonded parameters after conversion
- Original Message - From: ABEL Stephane 175950 stephane.a...@cea.fr Date: Monday, September 13, 2010 2:59 Subject: [gmx-users] charmm to gromacs nonbonded parameters after conversion To: gmx-users@gromacs.org Hi GMX users, I would like to perform MD with new developped CHARMM parameters in GROMACS. Since these parameters are new, they are not presents in the ffcharm*.itp files given in the of charmm27.ff in the latest GMX distribution. So I have already made the conversions for the bonded parameters. In case of the nonbonded parameters, I have added the LJ values for the new atom types at the end of the NONBONDED section of a par_all_27_lipid.prm file downloaded from the CHARMM website. To convert the LJ values in GROMACS format, I used the perl script of M. Abraham : convert_charmm_to_gromacs.pl (v.1.3) as follow : perl convert_charmm_to_gromacs.pl par_all27_lipid.prm I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected. In the ffcharmmnb.itp the [ atomtypes ] section is present but not the [ pairtypes ] section. Moreover the values in the [ atomtypes ] are different compared to same file given in latest GMX distrib (see below). Why these differences ? - My ffcharmmnb.itp file [ atomtypes ] ;name mass charge ptype c6 c12 CTL1 12.011000 0.0 A - 0.001485 -6.588e-06 ; -0.000252 -3.793e-07 CTL2 12.011000 0.0 A - 0.001978 -4.173e-06 ; -0.000252 -3.793e-07 CTL3 12.011000 0.0 A - 0.003011 -6.944e-06 ; -0.000252 -3.793e-07 CTL5 12.011000 0.0 A - 0.003274 -8.007e-06 ; -0.000252 -3.793e-07 CEL1 12.011000 0.0 A - 0.003035 -8.095e-06 -- GROMACS 4.5.1 ffcharmmnb.itp [ atomtypes ] ;name at.num mass charge ptype sigma epsilon CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 CTL2 6 12.01100 0.05 A 0.358141284692 0.234304 CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472 CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 . Thank in advance for your halp As the column headings note, the GROMACS 4.5 CHARMM27 uses sigma-epsilon VDW parameters, and my script converted to c6-c12 parameters. As you will see in the appropriate equations in chapter 3 or 4 of the manual, such numbers will be wildly different, but should produce the same energies and forces. 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
Re: [gmx-users] PBS script
I apologize to all for this, as I meant it to be a single reply; but as someone who has quietly watched the soon Dr. Lemkul bust his chops providing first class advice/assistance to any and all, usually w/in 15 min, everyday for years, I could not abide someone suggesting less than complete commitment to help on Justin's part. KSR On Sep 12, 2010, at 6:27 PM, KS Rotondi wrote: it must be hard to do your own research On Sep 12, 2010, at 5:52 PM, manoj singh wrote: Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 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
Re: [gmx-users] PBS script
:) I am basically a Charmm and Amber user and I have used Gromacs 3.X coupe of years ago. Now, for some reason I need to use Gromacs-4.x again. My old PBS script is not working anymore for this newer version for Gromacs. I just wanted to see if there is anything special required for the newer version for Gromacs and that is way I wanted to see a working script. Sincerely, On Sun, Sep 12, 2010 at 7:27 PM, KS Rotondi k...@chemistry.umass.edu wrote: I apologize to all for this, as I meant it to be a single reply; but as someone who has quietly watched the soon Dr. Lemkul bust his chops providing first class advice/assistance to any and all, usually w/in 15 min, everyday for years, I could not abide someone suggesting less than complete commitment to help on Justin's part. KSR On Sep 12, 2010, at 6:27 PM, KS Rotondi wrote: it must be hard to do your own research On Sep 12, 2010, at 5:52 PM, manoj singh wrote: Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: manoj singh wrote: Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Contact your system admins. There are far too many variables for such a setup for anyone here to send such information. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 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 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
Re: [gmx-users] PBS script
- Original Message - From: manoj singh mks.am...@gmail.com Date: Monday, September 13, 2010 11:17 Subject: Re: [gmx-users] PBS script To: Discussion list for GROMACS users gmx-users@gromacs.org :) I am basically a Charmm and Amber user and I have used Gromacs 3.X coupe of years ago. Now, for some reason I need to use Gromacs-4.x again. My old PBS script is not working anymore for this newer version for Gromacs. I just wanted to see if there is anything special required for the newer version for Gromacs and that is way I wanted to see a working script. OK, that's a bit different from someone wanting a script for the PBS side of things :-) The use of checkpoint files for restarts and no longer needing grompp -np for parallel runs are the two major changes. Search the GROMACS webpage for more discussion here. 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
Re: [gmx-users] PBS script
Hi Chris, Sorry if I have been rude is my response. I am new to the Gromacs-4.0. I just thought if some one can not give positive response to the query, that person should not be responding as this prohibits the further response to the topic. Again, thanks for your mail and sorry for my any irresponsible post. Manoj On Sun, Sep 12, 2010 at 6:25 PM, chris.ne...@utoronto.ca wrote: Manoj, to suggest that Justin is being lazy would be to ignore the hundreds, possibly thousands, of helpful posts that he has made on the gromacs mailing list to assist users like yourself free of charge. In fact, Justin was probably helping you more than you have realized by pointing out that you can access some of this information in places other than the gromacs mailing list, and yes, google is one of those places. Chris. -- original message -- Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalemkul at vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -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 thewww 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] PBS script
manoj singh wrote: Hi Chris, Sorry if I have been rude is my response. I am new to the Gromacs-4.0. I just thought if some one can not give positive response to the query, that person should not be responding as this prohibits the further response to the topic. There are no such rules here. Everyone is welcome to comment if they have insight or tips. My response was also not what I would call not positive, rather an effort to genuinely help point you in the right direction. In return, I received an insult. In general, no one on this list will spoon-feed someone a procedure (especially when it seems that the individual has not done their homework) as it simply requires too much time for a simple mailing list. Let's turn this situation into a learning experience. Your first post suggested that you knew nothing about PBS or how to use Gromacs. Based on your later posts, this is obviously not the case. To get an effective response, you should do the following: 1. Post the script you're trying to use. 2. Post error message you're getting (if any), or otherwise describe (or better yet, cut-and-paste) relevant output from your queuing software that indicates the problem. 3. Understand that if someone suggests and additional resource, don't take it as dismissive. You may simply be asking the wrong question, or perhaps asking the right question in the wrong place. If I simply post the PBS script for use with my cluster, then some unsuspecting user will probably later on stumble across that post, take it out of context, and then blindly assume that it is the only correct way to use Gromacs, and we perpetuate a cycle of confusion. For a few more tips: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin Again, thanks for your mail and sorry for my any irresponsible post. Manoj On Sun, Sep 12, 2010 at 6:25 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: Manoj, to suggest that Justin is being lazy would be to ignore the hundreds, possibly thousands, of helpful posts that he has made on the gromacs mailing list to assist users like yourself free of charge. In fact, Justin was probably helping you more than you have realized by pointing out that you can access some of this information in places other than the gromacs mailing list, and yes, google is one of those places. Chris. -- original message -- Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalemkul at vt.edu http://vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 thewww interface or send it to gmx-users-requ...@gromacs.org mailto: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
Re: [gmx-users] PBS script
Justin, Sorry if you felt insult. I was having trouble running the gromacs at that point and therefore turned to mailing in order to get some help. This topic seems to getting unnecessary attention of many, which I certainly did not want. I later found problem with mpdboot etc ( since this was compiled with mpich2), which I hope to fix tomorrow. So, please conclude this topic here. Sincerely, On Sun, Sep 12, 2010 at 10:33 PM, Justin A. Lemkul jalem...@vt.edu wrote: manoj singh wrote: Hi Chris, Sorry if I have been rude is my response. I am new to the Gromacs-4.0. I just thought if some one can not give positive response to the query, that person should not be responding as this prohibits the further response to the topic. There are no such rules here. Everyone is welcome to comment if they have insight or tips. My response was also not what I would call not positive, rather an effort to genuinely help point you in the right direction. In return, I received an insult. In general, no one on this list will spoon-feed someone a procedure (especially when it seems that the individual has not done their homework) as it simply requires too much time for a simple mailing list. Let's turn this situation into a learning experience. Your first post suggested that you knew nothing about PBS or how to use Gromacs. Based on your later posts, this is obviously not the case. To get an effective response, you should do the following: 1. Post the script you're trying to use. 2. Post error message you're getting (if any), or otherwise describe (or better yet, cut-and-paste) relevant output from your queuing software that indicates the problem. 3. Understand that if someone suggests and additional resource, don't take it as dismissive. You may simply be asking the wrong question, or perhaps asking the right question in the wrong place. If I simply post the PBS script for use with my cluster, then some unsuspecting user will probably later on stumble across that post, take it out of context, and then blindly assume that it is the only correct way to use Gromacs, and we perpetuate a cycle of confusion. For a few more tips: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin Again, thanks for your mail and sorry for my any irresponsible post. Manoj On Sun, Sep 12, 2010 at 6:25 PM, chris.ne...@utoronto.ca mailto: chris.ne...@utoronto.ca wrote: Manoj, to suggest that Justin is being lazy would be to ignore the hundreds, possibly thousands, of helpful posts that he has made on the gromacs mailing list to assist users like yourself free of charge. In fact, Justin was probably helping you more than you have realized by pointing out that you can access some of this information in places other than the gromacs mailing list, and yes, google is one of those places. Chris. -- original message -- Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul jalemkul at vt.edu http://vt.edu wrote: manoj singh wrote: Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. If you know enough to make changes, then you probably know enough to get up and running. A Google search for example PBS script turns up nearly 4 million results, the first of which contains much of the necessary basic information. -Justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 thewww interface or send it to gmx-users-requ...@gromacs.org mailto: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 mailing listgmx-users@gromacs.org
Re: [gmx-users] Re: Polyglycine PDB file.
On 2010-09-13 00.06, C Johnson wrote: I guess your pdb file has been damaged by a text editor (Word?). PDB files are fixed format, you can not add or remove spaces at will. You could try clicking together a peptide in Pymol or so, or drop the prodrg output in Notepad (if you're on Windows). On mac or linux it should be straightforward with text editors. I copied the PRODRG PDB into vim, changed HETATM to ATOM and DRG to GLY and renumbered the residues. I really don't understand what I could have done wrong. Can you get the file to convert with pdb2gmx? If you change HETATM into ATOM maintaining the spacing it should work. -- 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
