Re: [gmx-users] Question Regarding Hydrogen Database Error
On 2/4/17 8:21 PM, Elise White wrote: Dr. Lemkul, Thank you very much for you help! I just modified my aminoacids.rtp file and my .hdb file as you suggested and tried running the protein through pdb2gmx just to ensure there weren't any other errors. Unfortunately, another error message has popped up now which says, "Residue 48 named NMA of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file." This means that the atom names in the input .pdb file do not match what you have in the .rtp file. Change the atom names in the .pdb file so that they match. -Justin Do you have any suggestions as to how I can avoid this? I have attached the full error message below. gmx pdb2gmx -f 2MZ7_AA.pdb -o 2MZ7_AA.gro -ignh -ter -ff gromos53a6_atb -water spc Using the Gromos53a6_atb force field in directory gromos53a6_atb.ff Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.r2b Reading 2MZ7_AA.pdb... WARNING: all CONECT records are ignored Read 'STRUCTURE OF TAU(267-312) BOUND TO MICROTUBULES', 347 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 48 residues with 347 atoms chain #res #atoms 1 'A'48347 All occupancies are one Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/atomtypes.atp Atomtype 64 Reading residue database... (gromos53a6_atb) Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 109 Sorting it all out... Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.hdb Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.n.tdb Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'A' (347 atoms, 48 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 71 donors and 63 acceptors were found. There are 95 hydrogen bonds Will use HISE for residue 268 Will use HISE for residue 299 Identified residue ACE266 as a starting terminus. Identified residue NMA312 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS268 CYS291 NE222 SG192 CYS291 SG192 1.498 HIS299 NE2254 2.400 1.077 Select start terminus type for ACE-266 0: NH3+ 1: NH2 2: None 2 Start terminus ACE-266: None Select end terminus type for NMA-312 0: COO- 1: COOH 2: None 2 End terminus NMA-312: None Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. --- Program gmx pdb2gmx, VERSION 5.1.1 Source code file: /tmp/gromacs-20160831-84924-1rfxk36/gromacs-5.1.1/src/ gromacs/gmxpreprocess/pgutil.c, line: 127 Fatal error: Residue 48 named NMA of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file. -- == 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Question Regarding Hydrogen Database Error
Dr. Lemkul, Thank you very much for you help! I just modified my aminoacids.rtp file and my .hdb file as you suggested and tried running the protein through pdb2gmx just to ensure there weren't any other errors. Unfortunately, another error message has popped up now which says, "Residue 48 named NMA of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file." Do you have any suggestions as to how I can avoid this? I have attached the full error message below. gmx pdb2gmx -f 2MZ7_AA.pdb -o 2MZ7_AA.gro -ignh -ter -ff gromos53a6_atb -water spc Using the Gromos53a6_atb force field in directory gromos53a6_atb.ff Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.r2b Reading 2MZ7_AA.pdb... WARNING: all CONECT records are ignored Read 'STRUCTURE OF TAU(267-312) BOUND TO MICROTUBULES', 347 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 48 residues with 347 atoms chain #res #atoms 1 'A'48347 All occupancies are one Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/atomtypes.atp Atomtype 64 Reading residue database... (gromos53a6_atb) Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 109 Sorting it all out... Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.hdb Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.n.tdb Opening force field file /usr/local/bin/../Cellar/ gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'A' (347 atoms, 48 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 71 donors and 63 acceptors were found. There are 95 hydrogen bonds Will use HISE for residue 268 Will use HISE for residue 299 Identified residue ACE266 as a starting terminus. Identified residue NMA312 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS268 CYS291 NE222 SG192 CYS291 SG192 1.498 HIS299 NE2254 2.400 1.077 Select start terminus type for ACE-266 0: NH3+ 1: NH2 2: None 2 Start terminus ACE-266: None Select end terminus type for NMA-312 0: COO- 1: COOH 2: None 2 End terminus NMA-312: None Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. --- Program gmx pdb2gmx, VERSION 5.1.1 Source code file: /tmp/gromacs-20160831-84924-1rfxk36/gromacs-5.1.1/src/ gromacs/gmxpreprocess/pgutil.c, line: 127 Fatal error: Residue 48 named NMA of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file. -- 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] Topology error
On 2/4/17 1:03 AM, Mehreen Jan wrote: Hello, I want to simulate heme of hemoglobin.I am using Gromacs version 5.0.7. and force feild GROMOS 96 43a1 and spc water model.I built Heme topology on Prodrg and Swiss param but Prodrg doesnt accept heme while Swiss param give errors. Kindly tell me appropriate force feild which I should use and How to generate iron and oxygen topology? or any alternative which I should use.Heme topology is available in almost all force feilds but It is for FE2+ not for FE3+ and I want to simulate FE3+. If it is possible, kindly please generate topology for heme containing oxygen. I shall be really very thankful to you. You should not need external servers to generate a heme topology; GROMOS already supports it. It's called HEME and it's in the .rtp file. Connections to ligating residues should be recognized via existing entries in specbond.dat. It seems that multiple people are asking the same question, so hopefully everyone interested sees this post to avoid repetition. -Justin This is the ligand , the heme atom. HETATM 2341 FE HEM C1542 7.320 80.715 -5.955 1.00 25.63 Fe HETATM 2342 CHA HEM C1542 7.828 77.591 -5.047 1.00 23.39 C HETATM 2343 CHB HEM C1542 6.501 81.578 -2.733 1.00 23.47 C HETATM 2344 CHC HEM C1542 6.798 84.039 -6.886 1.00 22.00 C HETATM 2345 CHD HEM C1542 7.415 79.872 -9.275 1.00 20.35 C HETATM 2346 NA HEM C1542 7.232 79.764 -4.194 1.00 25.04 N HETATM 2347 C1A HEM C1542 7.469 78.413 -3.980 1.00 25.77 C HETATM 2348 C2A HEM C1542 7.236 78.109 -2.602 1.00 26.75 C HETATM 2349 C3A HEM C1542 6.841 79.239 -1.971 1.00 26.16 C HETATM 2350 C4A HEM C1542 6.845 80.286 -2.956 1.00 24.77 C HETATM 2351 CMA HEM C1542 6.512 79.509 -0.487 1.00 23.24 C HETATM 2352 CAA HEM C1542 7.389 76.695 -1.990 1.00 30.57 C HETATM 2353 CBA HEM C1542 8.749 76.200 -1.503 1.00 34.82 C HETATM 2354 CGA HEM C1542 8.827 74.825 -0.843 1.00 37.87 C HETATM 2355 O1A HEM C1542 7.934 73.913 -0.680 1.00 39.74 O HETATM 2356 O2A HEM C1542 10.021 74.626 -0.423 1.00 40.42 O HETATM 2357 NB HEM C1542 6.751 82.455 -4.998 1.00 23.10 N HETATM 2358 C1B HEM C1542 6.460 82.611 -3.660 1.00 22.37 C HETATM 2359 C2B HEM C1542 6.131 83.997 -3.367 1.00 21.40 C HETATM 2360 C3B HEM C1542 6.235 84.681 -4.510 1.00 21.71 C HETATM 2361 C4B HEM C1542 6.614 83.714 -5.544 1.00 21.85 C HETATM 2362 CMB HEM C1542 5.830 84.540 -1.947 1.00 20.77 C HETATM 2363 CAB HEM C1542 6.009 86.177 -4.817 1.00 20.85 C HETATM 2364 CBB HEM C1542 4.894 86.822 -4.391 1.00 21.93 C HETATM 2365 NC HEM C1542 7.180 81.751 -7.717 1.00 23.07 N HETATM 2366 C1C HEM C1542 6.859 83.099 -7.910 1.00 21.16 C HETATM 2367 C2C HEM C1542 6.559 83.360 -9.301 1.00 19.55 C HETATM 2368 C3C HEM C1542 6.724 82.197 -9.967 1.00 19.24 C HETATM 2369 C4C HEM C1542 7.132 81.190 -9.023 1.00 21.12 C HETATM 2370 CMC HEM C1542 6.119 84.748 -9.815 1.00 17.45 C HETATM 2371 CAC HEM C1542 6.506 81.891 -11.455 1.00 17.62 C HETATM 2372 CBC HEM C1542 5.616 82.527 -12.236 1.00 18.11 C HETATM 2373 ND HEM C1542 7.593 79.010 -6.981 1.00 22.41 N HETATM 2374 C1D HEM C1542 7.635 78.876 -8.352 1.00 21.08 C HETATM 2375 C2D HEM C1542 7.835 77.476 -8.654 1.00 21.66 C HETATM 2376 C3D HEM C1542 7.913 76.830 -7.505 1.00 21.01 C HETATM 2377 C4D HEM C1542 7.763 77.760 -6.423 1.00 22.07 C HETATM 2378 CMD HEM C1542 7.919 76.887 -10.102 1.00 20.29 C HETATM 2379 CAD HEM C1542 8.131 75.321 -7.321 1.00 20.98 C HETATM 2380 CBD HEM C1542 6.723 74.752 -7.027 1.00 23.17 C HETATM 2381 CGD HEM C1542 6.768 73.298 -6.794 1.00 24.91 C HETATM 2382 O1D HEM C1542 6.242 72.753 -5.808 1.00 29.44 O HETATM 2383 O2D HEM C1542 7.406 72.657 -7.630 1.00 26.84 O HETATM 2384 HHA HEM C1542 8.236 76.638 -4.744 1.00 0.00 H HETATM 2385 HHB HEM C1542 6.228 81.833 -1.720 1.00 0.00 H HETATM 2386 HHC HEM C1542 6.899 85.082 -7.147 1.00 0.00 H HETATM 2387 HHD HEM C1542 7.471 79.584 -10.314 1.00 0.00 H HETATM 2388 HMA1 HEM C1542 5.559 79.043 -0.235 1.00 0.00 H HETATM 2389 HMA2 HEM C1542 7.298 79.091 0.141 1.00 0.00 H HETATM 2390 HMA3 HEM C1542 6.446 80.584 -0.319 1.00 0.00 H HETATM 2391 HAA2 HEM C1542 7.055 75.989 -2.750 1.00 0.00 H HETATM 2392 HAA3 HEM C1542 6.696 76.625 -1.151 1.00 0.00 H HETATM 2393 HBA2 HEM C1542 9.413 76.181 -2.367 1.00 0.00 H HETATM 2394 HBA3 HEM C1542 9.139 76.933 -0.797 1.00 0.00 H HETATM 2395 HMB1 HEM C1542 6.754 84.582 -1.370 1.00 0.00 H HETATM 2396 HMB2 HEM C1542 5.404 85.541 -2.024 1.00 0.00 H HETATM 2397 HMB3 HEM C1542 5.120 83.880 -1.449 1.
Re: [gmx-users] Question Regarding Hydrogen Database Error
On 2/4/17 7:00 PM, Elise White wrote: Hello everyone, I am a junior at Binghamton High School amidst researching the Tau protein through various biomolecular simulations and studies. Recently, I introduced the NMA capping group to the force field I am working with - Gromos96 53a6 - by properly adding it to the residuetypes.dat file and adjusting the aminoacids.rtp file as depicted below based on a topology of NMA I generated using the ATB. As far as I'm concerned, this process was successful, as GROMACS recognized the capping group. [ NMA ] [ atoms ] H H 0.258 1 N N -1.331 2 CA CH3 0.571 3 1HA H -0.166 4 2HA H -0.166 5 3HA H -0.166 6 These charges add up to -1, so something has gone wrong. Moreover, since Gromos96 is a united-atom force field, I have doubts about whether or not there should even be H atoms on this carbon. The point of a capping group is to mimic a peptide bond, and the CH3 is an analog to the alpha-carbon of an amino acid. Gromos96 treats such carbons as uncharged. You also won't be able to generate H atoms that are named with integers as the first character, but again I don't think they should be there. Their types are also wrong, as H is a polar H atom (e.g. -NH or -OH groups) so this isn't correct, in addition to the fact that a CH3 atom type means you don't have H attached to that carbon. I'm not sure why ATB would give you such a topology, but something seems fishy, starting from the very charges themselves. [ bonds ] H N NCA CA 1HA CA 2HA CA 3HA [ angles ] H NCA NCA 1HA NCA 2HA NCA 3HA 1HACA 2HA 1HACA 3HA 2HACA 3HA However, an error message popped up notifying me that I need to update the hydrogen database with the 3 tetrahedral hydrogens attached to the alpha carbon- 1HA, 2HA, and 3HA. I read chapter 5.6.4 of the manual thoroughly several times, and I am still incredibly confused about what a "control atom" is - and am quite unsure about what "control atoms" I need to specify before adding my 3 tetrahedral hydrogens. "Control atoms" are atoms that can be used to define a local geometry, i.e. there is a simple internal coordinate builder that adds H atoms based on the relative positions of existing atoms. For CHARMM, our NMA capping group (which is named NME to avoid a clash with the N-methylacetamide group) is: NME 2 1 1 HN N -C CH3 3 4 HH3 CH3 N -C I would expect a Gromos96 NMA .rtp file to look more like: [ NMA ] [ atoms ] H H 0.310 1 N N -0.310 2 CA CH3 0.000 3 [ bonds ] N H N CA with an .hdb entry of NMA 1 1 1 H N -C CH3 It should be rather simple. -Justin It is my hope that one of you vastly experienced computational biochemists could point me in the right direction or clarify my understanding. I appreciate you reading my message - it is truly an honor - I respect and admire all of you. Best regards, Elise White -- == 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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
[gmx-users] Question Regarding Hydrogen Database Error
Hello everyone, I am a junior at Binghamton High School amidst researching the Tau protein through various biomolecular simulations and studies. Recently, I introduced the NMA capping group to the force field I am working with - Gromos96 53a6 - by properly adding it to the residuetypes.dat file and adjusting the aminoacids.rtp file as depicted below based on a topology of NMA I generated using the ATB. As far as I'm concerned, this process was successful, as GROMACS recognized the capping group. [ NMA ] [ atoms ] H H 0.258 1 N N -1.331 2 CA CH3 0.571 3 1HA H -0.166 4 2HA H -0.166 5 3HA H -0.166 6 [ bonds ] H N NCA CA 1HA CA 2HA CA 3HA [ angles ] H NCA NCA 1HA NCA 2HA NCA 3HA 1HACA 2HA 1HACA 3HA 2HACA 3HA However, an error message popped up notifying me that I need to update the hydrogen database with the 3 tetrahedral hydrogens attached to the alpha carbon- 1HA, 2HA, and 3HA. I read chapter 5.6.4 of the manual thoroughly several times, and I am still incredibly confused about what a "control atom" is - and am quite unsure about what "control atoms" I need to specify before adding my 3 tetrahedral hydrogens. It is my hope that one of you vastly experienced computational biochemists could point me in the right direction or clarify my understanding. I appreciate you reading my message - it is truly an honor - I respect and admire all of you. Best regards, Elise White -- 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] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates
Awesome Mark, thanks! It works. I filed a bug about a nonexistent -clustercenter option mentioned in the v5.1.2 help file, but the command seems to work anyway for my usage. Thanks again, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 04 February 2017 07:27:52 To: Discussion list for GROMACS users Subject: Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates Hi, I've never really use it myself, but I imagine trjconv -pbc cluster is useful for this kind of scenario when you want to treat a group of molecules as indivisible. Mark On Sat, 4 Feb 2017 09:33 Christopher Neale wrote: > Dear users: > > I have a system in which molecule A is in direct contact with molecule B. > However, molecule B is imaged in a different periodic cell. What I would > like to do is to get an image of both molecules in a periodic > representation in which they actually are in contact (i.e., reimage > molecule B such that it is closest to molecule A). However, I do not want > to lose spatial information with e.g. a trjconv -center -pbc mol command. > > This is part of a complex automated build procedure and I can get into > more details if that is useful, but the crux is that I am extracting a > frame from a simulation, building more atoms onto molecule A, and setting > up a new simulation. To build onto molecule A, I want to then do a vacuum > EM before adding it back to the water box, for which I first enlarge the > vacuum box, and changing box dimensions is messing with the periodicity and > throwing molecule B away from molecule A in an unrealistic fashion > (molecule B is a tightly bound ligand). > > I could do what I want by breaking each molecule out into its own box, > checking for contacts, reimaging, and then putting them back together. I > presume (but have not checked) that I could also do this by making a new > .itp file in which both molecule A and B are part of the same [ molecule ] > definition and then running a zero-step mdrun. However, I am writing to see > if anybody knows how reimage based on a selection (would be a single atom > in molecule A near the contact between molecule A and B) more elegantly > with processing tools available in gromacs. > > Thank you for your help, > Chris. > -- > 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.
Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates
Hi, I've never really use it myself, but I imagine trjconv -pbc cluster is useful for this kind of scenario when you want to treat a group of molecules as indivisible. Mark On Sat, 4 Feb 2017 09:33 Christopher Neale wrote: > Dear users: > > I have a system in which molecule A is in direct contact with molecule B. > However, molecule B is imaged in a different periodic cell. What I would > like to do is to get an image of both molecules in a periodic > representation in which they actually are in contact (i.e., reimage > molecule B such that it is closest to molecule A). However, I do not want > to lose spatial information with e.g. a trjconv -center -pbc mol command. > > This is part of a complex automated build procedure and I can get into > more details if that is useful, but the crux is that I am extracting a > frame from a simulation, building more atoms onto molecule A, and setting > up a new simulation. To build onto molecule A, I want to then do a vacuum > EM before adding it back to the water box, for which I first enlarge the > vacuum box, and changing box dimensions is messing with the periodicity and > throwing molecule B away from molecule A in an unrealistic fashion > (molecule B is a tightly bound ligand). > > I could do what I want by breaking each molecule out into its own box, > checking for contacts, reimaging, and then putting them back together. I > presume (but have not checked) that I could also do this by making a new > .itp file in which both molecule A and B are part of the same [ molecule ] > definition and then running a zero-step mdrun. However, I am writing to see > if anybody knows how reimage based on a selection (would be a single atom > in molecule A near the contact between molecule A and B) more elegantly > with processing tools available in gromacs. > > Thank you for your help, > Chris. > -- > 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.
Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")
Dear Mark, I built and ran it on the same machine. The test conclusion of $builddir/bin/mdrun-test is: [--] Global test environment tear-down [==] 24 tests from 8 test cases ran. (5206 ms total) [ PASSED ] 24 tests. I searched the complete test result of mdrun-rest (which is quite long), but did not find "SIMD" (or Simd, simd). Thanks. Qing At 2017-02-03 21:12:15, "Mark Abraham" wrote: >Hi, > >Surprising, but we don't test on (or officially support) Cygwin, so could >happen. It would be most likely to happen if you built on a different >machine than you were running on... Does $builddir/bin/mdrun-test pass? >Does the terminal output mention SIMD? > >Mark > >On Fri, Feb 3, 2017 at 1:29 PM Qing Lv wrote: > >> Mark, >> >> >> The results are: >> $ ./simd-test.exe >> Segmentation fault (core dumped) >> >> >> Thanks, >> Qing >> >> >> At 2017-02-03 19:46:35, "Mark Abraham" wrote: >> >Hi, >> > >> >Unlikely, given that the other tests passed. But what is the output from >> >running that manually, e.g. $builddir/bin/simd-test >> > >> >Mark >> > >> >On Fri, Feb 3, 2017 at 6:52 AM Qing Lv wrote: >> > >> >> Thank you, Mark. I am now trying to install devtoolset-2. >> >> >> >> >> >> Regarding Cygwin version, I must clarify that, although the compilation >> is >> >> successful, I got an error message when performing "make check": >> >> 95% tests passed, 1 tests failed out of 20 >> >> The following tests FAILED: >> >> 12 - SimdUnitTests (SEGFAULT) >> >> Will it be a serious problem? >> >> Thanks. >> >> >> >> >> >> Qing >> >> >> >> >> >> At 2017-02-03 13:08:50, "Mark Abraham" >> wrote: >> >> >Hi, >> >> > >> >> >These are linking errors that look like they are from not linking the >> >> >appropriate version of the C++ standard library. I highly recommend >> >> leaving >> >> >the system libraries alone on redhat systems, and instead compiling >> with >> >> >the devtoolset packages. >> >> > >> >> >Thanks for the Cygwin report. People often report problems that look >> like >> >> >they come from broken systems, and we rarely hear of a resolution. >> >> > >> >> >Mark >> >> > >> >> >On Fri, 3 Feb 2017 05:55 Qing Lv wrote: >> >> > >> >> >> Hi Colleagues, >> >> >> >> >> >> >> >> >> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a >> Redhat >> >> 6.5 >> >> >> server; I have updated GCC compiler and all dependent libraries >> (tried >> >> GCC >> >> >> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC >> 4.4.7, >> >> >> which is too old.) >> >> >> I used the commmand >> >> >> export CC=gcc >> >> >> export CXX=gcc >> >> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON >> >> >> # No errors reported till now >> >> >> make >> >> >> When 100% completed, I got a lot of error messages like >> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to >> >> >> ‘std::runtime_error::what() const’ >> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to >> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to >> >> >> And the error messages finished with >> >> >> collect2: Error: ld returns 1 >> >> >> make[2]: *** [bin/template] Error 1 >> >> >> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 >> >> >> make: *** [all] Error 2 >> >> >> >> >> >> >> >> >> Any friends can help? Thanks >> >> >> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin. >> >> >> >> >> >> >> >> >> Qing >> >> >> -- >> >> >> 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. >> >-- >> >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 >> >
[gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates
Dear users: I have a system in which molecule A is in direct contact with molecule B. However, molecule B is imaged in a different periodic cell. What I would like to do is to get an image of both molecules in a periodic representation in which they actually are in contact (i.e., reimage molecule B such that it is closest to molecule A). However, I do not want to lose spatial information with e.g. a trjconv -center -pbc mol command. This is part of a complex automated build procedure and I can get into more details if that is useful, but the crux is that I am extracting a frame from a simulation, building more atoms onto molecule A, and setting up a new simulation. To build onto molecule A, I want to then do a vacuum EM before adding it back to the water box, for which I first enlarge the vacuum box, and changing box dimensions is messing with the periodicity and throwing molecule B away from molecule A in an unrealistic fashion (molecule B is a tightly bound ligand). I could do what I want by breaking each molecule out into its own box, checking for contacts, reimaging, and then putting them back together. I presume (but have not checked) that I could also do this by making a new .itp file in which both molecule A and B are part of the same [ molecule ] definition and then running a zero-step mdrun. However, I am writing to see if anybody knows how reimage based on a selection (would be a single atom in molecule A near the contact between molecule A and B) more elegantly with processing tools available in gromacs. Thank you for your help, Chris. -- 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.