[gmx-users] Installtion of gromacs-4.5.3
Hi... I am try to istalling gromacs -4.5.3 on AMD phenom II. I am following the installtions protocols, 1 St i have installed the fftw3.2.2, ./configure --enable-threads --enables-floats --enables-sse make make install then I am doing the "cmake". cd gromacs-4.5.3 mkdir exec cd exec cmake ../ After cmake the make -j 6 gives me an error "Linking C shared library libmd.so /usr/bin/ld: /usr/local/lib/libfftw3f.a(tensor.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2" please suggest me what I should do next... with regards Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India.-- 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] carbohydrate parameters in ffG53a6
Hi Jianhui, For your sugar part you can use PRODRG, which will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS and from literature if you can find out the parameters of ffG53a6 force field, then you can correct the charge, angle and dihedral values that you are collected from the PRODRG. Hope this will help you. Regards... Parichita... Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. --- On Wed, 18/8/10, Jianhui Tian wrote: From: Jianhui Tian Subject: [gmx-users] carbohydrate parameters in ffG53a6 To: gmx-users@gromacs.org Date: Wednesday, 18 August, 2010, 10:16 AM Hi, I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the Gromacs force field for glycolipid? Jianhui -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] MD simulation of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Hi Somer, I want to simulate my Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose explicitly using my NOE restrain. I am new to MD using GROMACS . Please,give some thought . Thanks in advance parichita Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - Save all your chat conversations. Find them online.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. So my questions are; 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care of hydrogens sitting on carbon atoms in a sugar molecule explicitly? 2- How can I most reliably produce topologies for my disaccharide that will be placed in a water box to perform MD? I am quite new to MD methods therefore I apologize already now if I put forward something incoherent. Thanks for the help, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background about simulating molecular systems. Chapter 5 is a must. If you continue on this path, note that sugar dihedrals, especially the ones connecting the rings, are complex. Check out Roberto Lins' paper on the 45a3 force field. Tsjerk On 9/17/07, Mark Abraham wrote: > parichita parichita wrote: > > Hi again. > > Thank you for your help > > I found my MANA in the ffG53a5.rtp and i can prepare > > the .gro and .top file from pdb2gmx. > > Now , i am facing another problem after solvation of > > my solute when i run the minimization the 1-6 linkage > > was broken .. > > please help me out > > "linkage was broken" doesn't help us help you. Please describe in detail > what you observed and why you think it was wrong. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - Save all your chat conversations. Find them online.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out thanks in advance! parichita. --- TJ Piggot <[EMAIL PROTECTED]> wrote: > Just a quick look at the ffG45a3.rtp shows that > there is an entry for ADE, > however the ADE entry is for Adenine. > > For help with your problem check out: > > http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database > > Tom > > --On Friday, September 14, 2007 14:13:55 +0100 > parichita parichita > <[EMAIL PROTECTED]> wrote: > > > Hi, > > > > I have facing some problem when converting > .pdb file to .gro and > > .top . > > I have a .pdb of alpha d-mannose (1-6) alpha > d-mannose. I was using the > > pdb2gmx command and 45a3 forcefield . > > Showing the fatal error: > > Atom O in residue ADE 1 not found in rtp entry > with 25 atoms > > while sorting atoms > > and > > Warning: 'ADMA' not found in residue topology > database, trying to use > > 'ADE' > > Warning: 'ADMA' not found in residue topology > database, trying to use > > 'ADE > > > > > > but in ffG45a3.rtp I could not found any ADE > ... > > so I was confused ... > > Please give me some suggession. > > The format of my M6M.pdb is, > > > > ATOM 1 C5 ADMA1 3.337 1.774 > -8.944 1.00 0.00 > > C > > ATOM 2 O ADMA1 4.702 1.679 > -8.463 1.00 0.00 > > O > > ATOM 3 C1 ADMA1 5.227 0.338 > -8.248 1.00 0.00 > > C > > ATOM 4 C2 ADMA1 4.345 -0.412 > -7.222 1.00 0.00 > > C > > ATOM 5 O2 ADMA1 4.481 0.211 > -5.965 1.00 0.00 > > O > > ATOM 6 C3 ADMA1 2.854 -0.372 > -7.633 1.00 0.00 > > C > > ATOM 7 O3 ADMA1 2.063 -0.925 > -6.611 1.00 0.00 > > O > > ATOM 8 C4 ADMA1 2.367 1.065 > -7.950 1.00 0.00 > > C > > ATOM 9 O4 ADMA1 1.062 1.009 > -8.476 1.00 0.00 > > O > > ATOM 10 C6 ADMA1 3.018 3.281 > -9.160 1.00 0.00 > > C > > ATOM 11 O6 ADMA1 1.778 3.456 > -9.811 1.00 0.00 > > O > > ATOM 12 H5 ADMA1 3.271 1.274 > -9.929 1.00 0.00 > > H > > ATOM 13 H1 ADMA1 6.262 0.415 > -7.876 1.00 0.00 > > H > > ATOM 14 H2 ADMA1 4.685 -1.464 > -7.133 1.00 0.00 > > H > > ATOM 15 HO2 ADMA1 5.425 0.166 > -5.725 1.00 0.00 > > H > > ATOM 16 H3 ADMA1 2.727 -0.987 > -8.546 1.00 0.00 > > H > > ATOM 17 HO3 ADMA1 1.139 -0.907 > -6.925 1.00 0.00 > > H > > ATOM 18 H4 ADMA1 2.343 1.645 > -7.006 1.00 0.00 > > H > > ATOM 19 HO4 ADMA1 0.779 1.926 > -8.640 1.00 0.00 > > H > > ATOM 20 1H6 ADMA1 3.805 3.735 > -9.772 1.00 0.00 > > H > > ATOM 21 2H6 ADMA1 3.014 3.809 > -8.202 1.00 0.00 > > H > > ATOM 22 H6 ADMA1 1.654 4.401 > -9.918 1.00 0.00 > > H > > ATOM 23 C5 ADMA1B 5.806 -2.519 > -10.516 1.00 0.00 > > C > > ATOM 24 O ADMA1B 6.529 -3.735 > -10.196 1.00 0.00 > > O > > ATOM 25 C1 ADMA1B 6.753 -4.668 > -11.291 1.00 0.00 > > C > > ATOM 26 O1 ADMA1B 7.522 -4.046 > -12.268 1.00 0.00 > > O > > ATOM 27 C2 ADMA1B 5.398 -5.107 > -11.893 1.00 0.00 > > C > > ATOM 28 O2 ADMA1B 4.700 -5.870 > -10.935 1.00 0.00 > > O > > ATOM 29 C3 ADMA1B 4.533 -3.881 > -12.271 1.00 0.00 > > C > > ATOM 30 O3 ADMA1B 3.254 -4.305 > -12.671 1.00 0.00 > > O > > ATOM 31 C4 ADMA1B 4.406 -2.866 > -11.106 1.00 0.00 > > C > > ATOM 32 O4 ADMA1B 3.754 -1.706 > -11.569 1.00 0.00 > > O > > ATOM 33 C6 ADMA1B 5.743 -1.655 > -9.224 1.00 0.00 > > C > > ATOM 34 O6 ADMA1B 5.227 -0.368 > -9.490 1.00 0.00 > > O > > ATOM 35 H5 ADMA1B 6.383
[gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Hi, I have facing some problem when converting .pdb file to .gro and .top . I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the pdb2gmx command and 45a3 forcefield . Showing the fatal error: Atom O in residue ADE 1 not found in rtp entry with 25 atoms while sorting atoms and Warning: 'ADMA' not found in residue topology database, trying to use 'ADE' Warning: 'ADMA' not found in residue topology database, trying to use 'ADE but in ffG45a3.rtp I could not found any ADE ... so I was confused ... Please give me some suggession. The format of my M6M.pdb is, ATOM 1 C5 ADMA1 3.337 1.774 -8.944 1.00 0.00 C ATOM 2 O ADMA1 4.702 1.679 -8.463 1.00 0.00 O ATOM 3 C1 ADMA1 5.227 0.338 -8.248 1.00 0.00 C ATOM 4 C2 ADMA1 4.345 -0.412 -7.222 1.00 0.00 C ATOM 5 O2 ADMA1 4.481 0.211 -5.965 1.00 0.00 O ATOM 6 C3 ADMA1 2.854 -0.372 -7.633 1.00 0.00 C ATOM 7 O3 ADMA1 2.063 -0.925 -6.611 1.00 0.00 O ATOM 8 C4 ADMA1 2.367 1.065 -7.950 1.00 0.00 C ATOM 9 O4 ADMA1 1.062 1.009 -8.476 1.00 0.00 O ATOM 10 C6 ADMA1 3.018 3.281 -9.160 1.00 0.00 C ATOM 11 O6 ADMA1 1.778 3.456 -9.811 1.00 0.00 O ATOM 12 H5 ADMA1 3.271 1.274 -9.929 1.00 0.00 H ATOM 13 H1 ADMA1 6.262 0.415 -7.876 1.00 0.00 H ATOM 14 H2 ADMA1 4.685 -1.464 -7.133 1.00 0.00 H ATOM 15 HO2 ADMA1 5.425 0.166 -5.725 1.00 0.00 H ATOM 16 H3 ADMA1 2.727 -0.987 -8.546 1.00 0.00 H ATOM 17 HO3 ADMA1 1.139 -0.907 -6.925 1.00 0.00 H ATOM 18 H4 ADMA1 2.343 1.645 -7.006 1.00 0.00 H ATOM 19 HO4 ADMA1 0.779 1.926 -8.640 1.00 0.00 H ATOM 20 1H6 ADMA1 3.805 3.735 -9.772 1.00 0.00 H ATOM 21 2H6 ADMA1 3.014 3.809 -8.202 1.00 0.00 H ATOM 22 H6 ADMA1 1.654 4.401 -9.918 1.00 0.00H ATOM 23 C5 ADMA1B 5.806 -2.519 -10.516 1.00 0.00 C ATOM 24 O ADMA1B 6.529 -3.735 -10.196 1.00 0.00 O ATOM 25 C1 ADMA1B 6.753 -4.668 -11.291 1.00 0.00 C ATOM 26 O1 ADMA1B 7.522 -4.046 -12.268 1.00 0.00 O ATOM 27 C2 ADMA1B 5.398 -5.107 -11.893 1.00 0.00 C ATOM 28 O2 ADMA1B 4.700 -5.870 -10.935 1.00 0.00 O ATOM 29 C3 ADMA1B 4.533 -3.881 -12.271 1.00 0.00 C ATOM 30 O3 ADMA1B 3.254 -4.305 -12.671 1.00 0.00 O ATOM 31 C4 ADMA1B 4.406 -2.866 -11.106 1.00 0.00 C ATOM 32 O4 ADMA1B 3.754 -1.706 -11.569 1.00 0.00 O ATOM 33 C6 ADMA1B 5.743 -1.655 -9.224 1.00 0.00 C ATOM 34 O6 ADMA1B 5.227 -0.368 -9.490 1.00 0.00 O ATOM 35 H5 ADMA1B 6.383 -1.951 -11.270 1.00 0.00 H ATOM 36 H1 ADMA1B 7.300 -5.545 -10.905 1.00 0.00 H ATOM 37 HO1 ADMA1B 7.013 -3.281 -12.602 1.00 0.00 H ATOM 38 H2 ADMA1B 5.572 -5.738 -12.788 1.00 0.00 H ATOM 39 HO2 ADMA1B 5.261 -6.638 -10.719 1.00 0.00 H ATOM 40 H3 ADMA1B 5.014 -3.365 -13.126 1.00 0.00 H ATOM 41 HO3 ADMA1B 2.756 -3.507 -12.928 1.00 0.00 H ATOM 42 H4 ADMA1B 3.788 -3.323 -10.307 1.00 0.00 H ATOM 43 HO4 ADMA1B 3.668 -1.103 -10.809 1.00 0.00 H ATOM 44 1H6 ADMA1B 6.749 -1.553 -8.805 1.00 0.00 H ATOM 45 2H6 ADMA1B 5.131 -2.153 -8.466 1.00 0.00 H TER thanks in advance .. parichita... Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or
