[gmx-users] how to know solvent molecule number
Hello, I want to do stimulation of my protein in solvent, ethanolamine (different percentage). I have made box of 1 nm and then using command "gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p topol.top", As per my knowledge, i solvated my protein in ethanolamine. Now I want to know the number of ethanolamine molecule present in box. Then I looked in to *.top* file but no information is availble in the file (SOL). (As per intruction, program is only hard-coded to update the topology in the case of water). I found increase in number of molecules from 7200 to 128004 in /home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro, respectively. It means something is inserted in box (must be ethanolamine!-my guess) How can i know number of ethanolamine molecules? for reference please find attched files. Thanking you in advance. -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Too many error at first step
Dear Justin, I updated Gromacs to 2016.2 but still, I am getting the same problem. I got following errors. 1. WARNING: all CONECT records are ignored 2. 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 454 residues with 3907 atoms 3. WARNING: there were 0 atoms with zero occupancy and 556 atoms with occupancy unequal to one (out of 3907 atoms). Check your pdb file. I hope you can help me. Thanking You Chintan On Mon, Jan 30, 2017 at 10:29 PM, Justin Lemkul <jalem...@vt.edu> 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=en >> ral=cbb.chin...@gmail.com=22> >> >> >> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul <jalem...@vt.edu> 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.r
Re: [gmx-users] Too many error at first step
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 <jalem...@vt.edu> 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=en >> ral=cbb.chin...@gmail.com=22> >> >> >> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul <jalem...@vt.edu> 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 2
Re: [gmx-users] Is .mdp file are same for each force field?
Thanks James for your valuable reply Thanking you Chintan On Feb 12, 2017 10:06 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote: > Hi Chintan, > > 1. No, all forcefields have different parameters that you need to take > into account in your .mdp files, especially non-bonded cut-offs such as > rlist and rvdw, which are an integral part of the forcefield. Certainly > you need to use a forcefield that includes zinc if you have zinc in your > protein (that said the error could also be that zinc is present but not be > called ZN in some forcefields). You can get bits of mdp files that are > forcefield-specific on the gromacs website e.g. > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM - you > can remove the /CHARMM and get a page to click through others. > > 2. Any mdp with constant temperature would need changing i.e. nvt.mdp, > npt.mdp and md.mdp - you should really read through the mdp files and > understand what's going on. Also look at > http://manual.gromacs.org/online/mdp_opt.html and there are options > related to temperature coupling. You may want to equilibrate to higher > temperature in steps by copying nvt.mdp and changing each one to have > progressively higher values. > > Best wishes > James > > > Dear gromacs user, > > > > I practiced of MD stimulation with LysoZyme tutorial. Now, They used 15: > > OPLS-AA/L force field and also i saved all *.mdp* file (ions. mdp, > md.mdp, > > nvt.mdp, npt.mdp, minim.mdp, etc.) as given in tutorial and successfully > > performed MD stimulation. > > > > Now, I have want to study my protein. I found force field 9 to 14 are > > reported for my protein in literature. Further, I also tried it and found > > "Residue 'ZN' not found in residue topology database" only for force > field > > 15 (OPLS-AA/L force field), not for any other force field (9 to 14). > > > > > > > > *Now, I have two questions.* > > > > *1) Can i use this file for stimulation study with other force field (9 > to > > 14)? If not, from where i get them?* > > *2) Also want to study MD at higher temperature, still Can i use tutorial > > .mdp files? or what informations i have to change in files (.mdp)* > > > > Can any one tell me what to do? > > > > > > -- > > Regards, > > Chintan Bhagat > > Research scholar, > > V.N.S.G.U, 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 gmx-users-requ...@gromacs.org. > > > > > -- > 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. > -- 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] Is .mdp file are same for each force field?
Dear gromacs user, I practiced of MD stimulation with LysoZyme tutorial. Now, They used 15: OPLS-AA/L force field and also i saved all *.mdp* file (ions. mdp, md.mdp, nvt.mdp, npt.mdp, minim.mdp, etc.) as given in tutorial and successfully performed MD stimulation. Now, I have want to study my protein. I found force field 9 to 14 are reported for my protein in literature. Further, I also tried it and found "Residue 'ZN' not found in residue topology database" only for force field 15 (OPLS-AA/L force field), not for any other force field (9 to 14). *Now, I have two questions.* *1) Can i use this file for stimulation study with other force field (9 to 14)? If not, from where i get them?* *2) Also want to study MD at higher temperature, still Can i use tutorial .mdp files? or what informations i have to change in files (.mdp)* Can any one tell me what to do? -- Regards, Chintan Bhagat Research scholar, V.N.S.G.U, 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 gmx-users-requ...@gromacs.org.
[gmx-users] Good force field for protein/metalloenzyme - GROMOS96 53a5, GROMOS96 43a2 or OPLS-AA/L
Dear all, I am new to gromacs and I want to know which force field is more appropriate for protein. I found in literature GROMOS96 53a5, GROMOS96 43a2 and OPLS-AA/L are suitable for my interest of protein. Can anyone suggest me which are the necessary things one need to check before the start? Moreover, I did not found any error using GROMOS96 53a5 and GROMOS96 43a2 in the first step. I found missing residue error while running OPLS-AA/L (*Residue 'ZN' not found in residue topology database)* -- Regards, Chintan Bhagat <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature=en=cbb.chin...@gmail.com=22> -- 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] Too many error at first step
Hello Justin, Which force field should I use? Further, How to check the compatibility of protein for force field? PDB id of my protein is 4g7a. Secondly, I am using Gromacs VERSION 5.1.4 which is most updated. Thanking you, Chinatn <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature=en=cbb.chin...@gmail.com=22> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul <jalem...@vt.edu> 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 >> Iden
[gmx-users] Too many error at first step
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$ -- Regards, Chintan Bhagat Mob. +91 88 66 61 11 49 <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature=en=cbb.chin...@gmail.com=22> -- 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] Mixed Solvation - MEA and water
Hello All, I am new to gromacs and I found it is very good software for MD study. Now, I want to study the effect of various concentration of MEA (30% to 70%) on my enzyme. My system contains only MEA and water in different ratio. Can any one help to write the script or run procedure? -- Regards, Chintan -- Regards, Chintan Bhagat Mob. +91 88 66 61 11 49 <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature=en=cbb.chin...@gmail.com=22> -- 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.
