Dear Justin, Thank you for your reply.
I selected my protein for MD study and I did the stimulation same as mentioned in lysozyme tutorial *using force field - GROMOS96 43a1 force field *(As, I came to know all force field has different .mdp file, so results are not vaild). I did the same as mention in tutorial (using .mdp fie). But, When i selected OPLS-AA/L all-atom force field, I got error message,* Residue 'ZN' not found in residue topology database*. Later, I search on literature, I found chaining ZN to MG is good and will does not make any significance changes in result. So, I replaced ZN by MG in my file and run the stimulation using OPLS-AA/L all-atom force field ( https://www.researchgate.net/post/How_can_I_rectify_this_error_Atom_type_Zn2_residue_ZN_not_found_in_atomtype_database). This time, I did not got any error or warning message. As, I am new, I am not sure, I am doing right or not . I also search for for adding residue to force field file, but not able do well ( http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field). I request you to suggest me whether I am doing right or not? (As, I am not expert!!!!!!) hope you reply. On Mon, Jan 30, 2017 at 10:29 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/30/17 11:54 AM, Chintan Bhagat wrote: > >> Hello Justin, >> >> Which force field should I use? >> > > One that supports what you need. I don't mean that to be dismissive; it's > your job in designing your research to look at the pros and cons of each > force field, and no one can or should make that (very critical) decision > for you. Has it been demonstrated to be effective for similar systems? > What are the limitations? > > Further, How to check the compatibility of protein for force field? PDB id >> of my protein is 4g7a. >> > > The protein isn't the issue. Every force field in GROMACS will handle the > protein. But Zn is another matter. This again requires an investigation > and assessment of the literature. > > Secondly, I am using Gromacs VERSION 5.1.4 which is most updated. >> >> > No, version 2016.1 is the latest, and I personally fixed the bug I > referred to for this version after 5.1.4 was released. Trust me, I'm > trying to help you avoid a very serious serious bug :) > > -Justin > > Thanking you, >> Chinatn >> >> >> >> <https://mailtrack.io/>Sent with Mailtrack >> <https://mailtrack.io/install?source=signature&lang=en&refer >> [email protected]&idSignature=22> >> >> >> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 1/30/17 11:08 AM, Chintan Bhagat wrote: >>> >>> Hello all, >>>> >>>> I am new to Gromacs, and I completed the Lysozyme tutorial. But When I >>>> started stimulation with my own protein, I got many errors. I am not >>>> understanding what to do? >>>> >>>> For error >>>> ------------------------------------------------------------ >>>> --------------------------------------------------------- >>>> >>>> lab@lab-desktop:~/Desktop/MD_tutorial$ gmx pdb2gmx -f 4g7a.pdb -o >>>> 4g7a_processed.gro -water spce >>>> . >>>> . >>>> . >>>> . >>>> . >>>> ........ >>>> gmx pdb2gmx -f 4g7a.pdb -o 4g7a_processed.gro -water spce >>>> >>>> >>>> Select the Force Field: >>>> From '/usr/local/gromacs/share/gromacs/top': >>>> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, >>>> 1999-2012, 2003) >>>> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) >>>> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, >>>> 461-469, 1996) >>>> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, >>>> 1049-1074, 2000) >>>> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, >>>> 712-725, >>>> 2006) >>>> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., >>>> Proteins 78, 1950-58, 2010) >>>> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) >>>> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) >>>> 9: GROMOS96 43a1 force field >>>> 10: GROMOS96 43a2 force field (improved alkane dihedrals) >>>> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >>>> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >>>> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >>>> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, >>>> DOI: >>>> 10.1007/s00249-011-0700-9) >>>> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >>>> 15 >>>> >>>> Using the Oplsaa force field in directory oplsaa.ff >>>> >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b >>>> Reading 4g7a.pdb... >>>> >>>> *WARNING: all CONECT records are ignored* >>>> Read 'CARBONATE DEHYDRATASE', 3726 atoms >>>> Analyzing pdb file >>>> Splitting chemical chains based on TER records or chain id changing. >>>> >>>> *WARNING: Chain identifier 'A' is used in two non-sequential blocks*. >>>> They will be treated as separate chains unless you reorder your file. >>>> >>>> *WARNING: Chain identifier 'B' is used in two non-sequential blocks.* >>>> They will be treated as separate chains unless you reorder your file. >>>> There are 4 chains and 0 blocks of water and 453 residues with 3726 >>>> atoms >>>> >>>> chain #res <https://plus.google.com/u/0/s/%23res> #atoms >>>> <https://plus.google.com/u/0/s/%23atoms> >>>> 1 'A' 224 1850 >>>> 2 'B' 225 1848 >>>> 3 'A' 2 14 >>>> 4 'B' 2 14 >>>> >>>> >>>> >>>> *WARNING: there were 0 atoms with zero occupancy and 24 atoms >>>> withoccupancy >>>> unequal to one (out of 3726 atoms). Check your pdb file.* >>>> >>>> >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp >>>> Atomtype 814 >>>> Reading residue database... (oplsaa) >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp >>>> Residue 51 >>>> Sorting it all out... >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb >>>> Opening force field file >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb >>>> Processing chain 1 'A' (1850 atoms, 224 residues) >>>> Analysing hydrogen-bonding network for automated assignment of histidine >>>> protonation. 348 donors and 340 acceptors were found. >>>> There are 571 hydrogen bonds >>>> Will use HISE for residue 13 >>>> Will use HISE for residue 64 >>>> Will use HISD for residue 89 >>>> Will use HISD for residue 91 >>>> Will use HISH for residue 96 >>>> Will use HISE for residue 108 >>>> Will use HISE for residue 111 >>>> Identified residue GLU2 as a starting terminus. >>>> Identified residue PHE225 as a ending terminus. >>>> 8 out of 8 lines of specbond.dat converted successfully >>>> Special Atom Distance matrix: >>>> HIS13 CYS24 HIS64 HIS89 HIS91 HIS96 HIS108 >>>> NE2102 SG205 NE2537 NE2752 NE2773 NE2812 NE2920 >>>> CYS24 SG205 1.292 >>>> HIS64 NE2537 1.662 1.215 >>>> HIS89 NE2752 2.291 1.422 1.134 >>>> HIS91 NE2773 2.078 1.340 1.109 0.319 >>>> HIS96 NE2812 2.309 1.478 1.921 1.078 0.956 >>>> HIS108 NE2920 2.341 1.518 1.551 0.549 0.461 0.594 >>>> HIS111 NE2948 3.366 2.266 2.218 1.186 1.430 1.481 1.207 >>>> MET124 SD1042 2.668 2.087 2.115 1.201 1.040 0.821 0.722 >>>> MET167 SD1384 3.105 2.374 2.793 1.822 1.730 0.920 1.288 >>>> CYS178 SG1462 1.405 0.204 1.183 1.243 1.160 1.286 1.317 >>>> MET205 SD1680 2.313 1.909 1.145 0.868 0.772 1.646 1.112 >>>> HIS111 MET124 MET167 CYS178 >>>> NE2948 SD1042 SD1384 SG1462 >>>> MET124 SD1042 1.600 >>>> MET167 SD1384 1.756 0.956 >>>> CYS178 SG1462 2.083 1.895 2.189 >>>> MET205 SD1680 1.859 1.368 2.264 1.770 >>>> Linking CYS-24 SG-205 and CYS-178 SG-1462... >>>> Start terminus GLU-2: NH3+ >>>> End terminus PHE-225: COO- >>>> Checking for duplicate atoms.... >>>> Now there are 1838 atoms. Deleted 12 duplicates. >>>> Generating any missing hydrogen atoms and/or adding termini. >>>> Now there are 224 residues with 3714 atoms >>>> Chain time... >>>> Making bonds... >>>> Number of bonds was 3759, now 3759 >>>> Generating angles, dihedrals and pairs... >>>> Before cleaning: 9973 pairs >>>> Before cleaning: 10098 dihedrals >>>> Keeping all generated dihedrals >>>> Making cmap torsions... >>>> There are 10098 dihedrals, 698 impropers, 6858 angles >>>> 9913 pairs, 3759 bonds and 0 virtual sites >>>> Total mass 26036.211 a.m.u. >>>> Total charge 8.548 e >>>> Writing topology >>>> Processing chain 2 'B' (1848 atoms, 225 residues) >>>> Analysing hydrogen-bonding network for automated assignment of histidine >>>> protonation. 347 donors and 337 acceptors were found. >>>> There are 552 hydrogen bonds >>>> Will use HISE for residue 1 >>>> Will use HISE for residue 13 >>>> Will use HISE for residue 64 >>>> Will use HISD for residue 89 >>>> Will use HISD for residue 91 >>>> Will use HISH for residue 96 >>>> Will use HISE for residue 108 >>>> Will use HISH for residue 111 >>>> Identified residue HIS1 as a starting terminus. >>>> Identified residue PHE225 as a ending terminus. >>>> 8 out of 8 lines of specbond.dat converted successfully >>>> Special Atom Distance matrix: >>>> HIS1 HIS13 CYS24 HIS64 HIS89 HIS91 HIS96 >>>> NE210 NE2112 SG215 NE2541 NE2756 NE2777 NE2816 >>>> HIS13 NE2112 1.745 >>>> CYS24 SG215 1.666 1.257 >>>> HIS64 NE2541 0.500 1.577 1.214 >>>> HIS89 NE2756 1.514 2.190 1.415 1.130 >>>> HIS91 NE2777 1.489 1.982 1.344 1.115 0.315 >>>> HIS96 NE2816 2.357 2.227 1.484 1.924 1.081 0.956 >>>> HIS108 NE2918 1.946 2.252 1.526 1.555 0.551 0.459 0.601 >>>> HIS111 NE2946 2.566 3.262 2.242 2.196 1.172 1.412 1.483 >>>> MET124 SD1040 2.434 2.585 2.097 2.116 1.194 1.033 0.823 >>>> MET167 SD1382 3.228 3.066 2.419 2.830 1.853 1.758 0.958 >>>> CYS178 SG1460 1.659 1.358 0.203 1.185 1.238 1.166 1.291 >>>> MET205 SD1678 1.254 2.207 1.915 1.146 0.874 0.778 1.653 >>>> HIS108 HIS111 MET124 MET167 CYS178 >>>> NE2918 NE2946 SD1040 SD1382 SG1460 >>>> HIS111 NE2946 1.196 >>>> MET124 SD1040 0.711 1.581 >>>> MET167 SD1382 1.317 1.779 0.974 >>>> CYS178 SG1460 1.326 2.060 1.905 2.233 >>>> MET205 SD1678 1.116 1.849 1.369 2.293 1.779 >>>> Linking CYS-24 SG-215 and CYS-178 SG-1460... >>>> Start terminus HIS-1: NH3+ >>>> End terminus PHE-225: COO- >>>> Checking for duplicate atoms.... >>>> Generating any missing hydrogen atoms and/or adding termini. >>>> Now there are 225 residues with 3732 atoms >>>> Chain time... >>>> Making bonds... >>>> Number of bonds was 3778, now 3778 >>>> Generating angles, dihedrals and pairs... >>>> Before cleaning: 10019 pairs >>>> Before cleaning: 10149 dihedrals >>>> Keeping all generated dihedrals >>>> Making cmap torsions... >>>> There are 10149 dihedrals, 705 impropers, 6891 angles >>>> 9959 pairs, 3778 bonds and 0 virtual sites >>>> Total mass 26174.361 a.m.u. >>>> Total charge 9.548 e >>>> Writing topology >>>> Processing chain 3 'A' (14 atoms, 2 residues) >>>> Warning: Starting residue ZN301 in chain not identified as >>>> Protein/RNA/DNA. >>>> Warning: Starting residue AZM302 in chain not identified as >>>> Protein/RNA/DNA. >>>> Problem with chain definition, or missing terminal residues. >>>> This chain does not appear to contain a recognized chain molecule. >>>> If this is incorrect, you can edit residuetypes.dat to modify the >>>> behavior. >>>> 8 out of 8 lines of specbond.dat converted successfully >>>> >>>> ------------------------------------------------------- >>>> Program gmx pdb2gmx, VERSION 5.1.4 >>>> Source code file: >>>> /home/lab/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, line: 645 >>>> >>>> >>>> *Fatal error:Residue 'ZN' not found in residue topology database* >>>> For more information and tips for troubleshooting, please check the >>>> GROMACS >>>> website at http://www.gromacs.org/Documentation/Errors >>>> ------------------------------------------------------- >>>> >>>> lab@lab-desktop:~/Desktop/MD_tutorial$ >>>> >>>> >>>> OPLS-AA does not support Zn ions. You'll need to either import >>> parameters >>> from the literature (if they exist) or use a force field that does >>> support >>> it. >>> >>> The more immediate concern is the fractional charges on the chains. >>> There >>> was a bug that was fixed some time ago regarding incorrect histidine >>> charges. Please upgrade immediately to version 2016.1 if you want to use >>> OPLS-AA so you get correct files. The topology you're currently >>> producing >>> is incorrect. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> [email protected] | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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 [email protected]. >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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 [email protected]. > -- Regards, Chintan Bhagat Research scholar, Veer Narmad South Gujarat University, India -- 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 [email protected].
