Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Hello, Though I don't know the answer to your question, I can offer a workaround for the task. I have simulated such C-terminally amidated peptides in vacuum before and I performed the same analysis using the Hydrogen bonds plugin in VMD. Hope this helps. Cheers, Sahil On 2020-04-28 07:20, Neena Susan Eappen wrote: > Hello gromacs users, > > My peptide has an amide group at the C-terminus. Hydrogen bond analysis using > gmx hbond does not take into account H-bond donors (NH2) from the amide group > (Note: this NH2 is considered as a residue according to opls ff). What might > be happening here? > > Many thanks, > Neena -- 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] 12 bead mapping of lipid
Hello, I see the problem now. You are right, the backmapping files have the 13 bead POPS rather that the latest 12 bead POPS. As far as I know the backmapping files have not been publicly updated but you could try the Martini forum. If the exact lipid coordinates are absolutely essential to your results, I guess you might have to create a new map file yourself. Otherwise, if a lipid bilayer is all you seek, you could always add newer all atom lipids in the process of transformation. - Sahil On 2020-03-07 01:39, Rabeta Yeasmin wrote: > Hi, > > I have run some coarse-grained simulations in GROMACS and now I am trying > to learn converting back the system to all-atom. I have set up the > coarse-grained system in CHARMM-GUI, They did not provide the mapping files > and the mapping files all I found in MARTINI website has 13 beads for POPS, > but my system POPS has 12 beads. That's why I am looking for newest mapping > of POPS lipid. > Thanks. > > Rabeta Yeasmin -- 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] 12 bead mapping of lipid
Hello, Do you want to include the 12 bead POPS model in your Martini CG simulations? That is straightforward : Download the "itp" file to the directory with the "top" file and enter #include "martini_v2.0_POPS_02.itp" with the hash in the header of the ".top" file. That should be enough to be given as input to grompp. Sahil On 2020-03-06 22:52, Rabeta Yeasmin wrote: > Hi Dave, > > Thanks for your reply. I have seen the new topology file. But I am > wondering how can I get the mapping of the new POPS. Is there any way that > I can do it myself? > > Rabeta Yeasmin -- 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] charmm gui pdb to gro.
Hey, You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag allows for ignoring preexisting hydrogen atoms if that's really required. Cheers, Sahil On 2020-01-14 12:23, Yogesh Sharma wrote: > Greetings, > hey, I want to convert the charmm gui generated pdb (membrane + protein) to > gromacs readable file. charmm generated lipids contain hydrogen atoms and > naming differences. I tried doing it manually but couldnt succeed. Is there > any script available for atom renaming and reordering? > > I also tried manual packing of POPC molecules from this site ( > http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein > extracted from charmm gui bilayer builder but simulation was not successful > probably i couldnot pack it properly (didn't get any error though. packing > was performed using inflategro with shrinking to a final area of 74A^2). > Charmm gui generated output is working fine with water but I want to > perform complete simulation in 54A7 ff due to ligand parameters > availability. hence, i have to convert charmm gui generated output to gro > format. Is there any way around? -- 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] gmx distance
Hello, Put both the indices in the same file as [ A ] *atoms numbers of residue 130* [ B ] *atom numbers of residue 153* and save this file with a .ndx extension (e.g. dist.ndx). Now, provide that file name with the -n option in gmx distance. Upon execution, it will automatically ask you which index groups to use for distance calculation where you can provide A and B as inputs. Cheers On 2019-12-19 14:39, Emran Heshmati wrote: > Dear All > I am in trouble with gmx distance command. I want to calculate the distance > between two amino acids (residue 130 and residue 153) in a protein after > gromacs standard simulation. After generating of r130.ndx and r153.ndx > index files, I use this command: > gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall > dist.xvg -oh disthist.xvg -b 7 -e 10 > but don't list r130 and r153 as extra groups. Adding -n *.ndx option > didn't sole the problem. Any comment please. -- 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] Neutral arginine; Charmm
Hi, I am trying to use neutral arginine for my work. Since the well documented issues of nearly equivalent tautomeric protonated states, it has not been implemented in the charmm forcefield. So, as suggested by the charmm developers, I used methyl-guanidinium and Arginine as a starting point and created a new neutral molecule [ ARN ] and made all the appropriate changes wherever required. However, pdb2gmx is not working as expected. Issue 1: No double bond seen between NE and CZ Issue 2: HH12 missing with error Warning: Long Bond (66-68 = 4.12787 nm) the following are the residue parameters borrowed from MGU1 and ported to make neutral arginine. [ ARN ] [ atoms ] N NH1 -0.470 0 HN H 0.310 1 CA CT1 0.070 2 HA HB1 0.090 3 CB CT2 -0.180 4 HB1 HA2 0.090 5 HB2 HA2 0.090 6 CG CT2 -0.180 7 HG1 HA2 0.090 8 HG2 HA2 0.090 9 CD CT2 0.060 10 HD1 HA2 0.090 11 HD2 HA2 0.090 12 NE NG2D1 -0.860 13 CZ CG2N1 0.660 14 NH1 NG321 -0.600 15 HH11 HGPAM2 0.290 16 HH12 HGPAM2 0.290 17 NH2 NG321 -0.600 18 HH21 HGPAM2 0.290 19 HH22 HGPAM2 0.290 20 C C 0.510 21 O O -0.510 22 [ bonds ] CB CA CG CB CD CG NE CD CZ NE NH2 CZ N HN N CA C CA C +N CA HA CB HB1 CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 CZ NH1 NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 O C [ impropers ] N -C CA HN C CA +N O CZ NE NH1 NH2 NH1 HH11 HH12 CZ NH2 HH21 HH22 CZ [ cmap ] -C N CA C +N -- Sahil -- 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] amide-capped C-terminus; OPLS force field
Hi, >> You need to add ions in the system to neautralise. >> >> and i think -0.18 qtotal considered as zero. > > That is absolutely not the case. Rounding errors should never amount to 0.001 > or even less. Thank you for clarifying that Justin, that is what I also thought too > If the OP is looking at charges in ffnonbonded.itp, those are never used and > have no bearing on what should actually be defined in the topology. > > -Justin > > -- But this leaves me with the original problem. Is there no way to have an amide C terminus and yet maintain neutrality of the system (with of course qtotal for everything else = 0 in the topology file)? - Sahil -- 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] Disulphide bonded cyclic peptides
Hello, In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. Yes I figured eventually that it was a stupid question to ask :) Thank you so much. On 2019-12-03 13:44, Alessandra Villa wrote: > Hi > > On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall wrote: > > Thank you Alessandra. > > I am extremely grateful for your help. It worked! > > However, one last bit > > You suggested to > > use the one of the backbone > for your new entry (since you do not have a real termini) for CYS-1 > Nopls_238 -0.500 0 > Hopls_2410.300 0 > CAopls_224B 0.140 1 > > You could also directly change the charges in the top file. > Apart from the top file, where could have I specified the opls_X > atomtypes? In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. Best regards Alessandra > Best regards, > > Sahil > > On 2019-11-29 15:46, Alessandra Villa wrote: > >> Hi, >> >> On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote: >> >> Hello, >> >> Thank you for your suggestions, gave me some insight into my own work. >> However, the problem still persists. >> >> With the option -ignh, you request pdb2gmx to add H atom. Thus, if you > have already H atoms in the pdb I suggest to remove the option -ignh. > >> I had already tried removing the -ignh option before posting this here >> but did not find success. >> >> Did you try also without -ter? >> >> Removing the -ter option does not work in any combination. It always >> overrides everything else and breaks the cyclising peptide bond into >> NH3+ and COO-. >> >> . >> >> Another option could be to remove the extra H from gro/pdb file you got > from pdb2gmx, remove H, (if you want, fix the atom number using editconf), > >> then try to use the so obtained pdb/gro file as input to pdb2gmx (without >> -ter -ignh) >> >> So this also does not work. pdb2gmx breaks the peptide bond without the >> -ter option. >> >> I tried putting a new entry in the OPLS aminoacids.n.tdb file as you >> suggested. I used the opls_910 planar hydrogen for secondary amines as >> shown below >> >> [ CYS2-NH ] >> [ replace ] >> N opls_900 14.0027 -0.9 >> CA opls_912B 12.011 0.12 >> [ add ] >> 1 1 H N CA C >> opls_910 1.008 0.36 >> [ delete ] >> H > You got a charged system, probably because you have generated a new > entry > without accounting for the partial charge. > > As atomic charge and atom types I suggest to use the one of the backbone > for your new entry (since you do not have a real termini) for CYS-1 > Nopls_238 -0.500 0 > Hopls_2410.300 0 > CAopls_224B 0.140 1 > > You could also directly change the charges in the top file. > > I hope this solve the problem > Best regards > Alessandra > > Now I can get the peptide bond correctly but the system is charged. > > Output below: > > Identified residue CYS1 as a starting terminus. > Identified residue CYS6 as a ending terminus. > 2 out of 2 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS1 CYS1 CYS1 CYS6 CYS6 > N1 C3 SG6 N87 C89 > CYS1 C3 0.244 > CYS1 SG6 0.312 0.419 > CYS6 N87 0.335 0.510 0.486 > CYS6 C89 0.136 0.373 0.322 0.239 > CYS6 SG92 0.387 0.482 0.205 0.420 0.365 > Linking CYS-1 N-1 and CYS-6 C-89... > Linking CYS-1 SG-6 and CYS-6 SG-92... > Select start terminus type for CYS-1 > 0: CYS2-NH > 1: NH3+ > 2: ZWITTERION_NH3+ (only use with zwitterions containing exactly one > residue) > 3: NH2 > 4: None > 0 > Start terminus CYS-1: CYS2-NH > Select end terminus type for CYS-6 > 0: COO- > 1: ZWITTERION_COO- (only use with zwitterions containing exactly one > residue) > 2: COOH > 3: None > 3 > End terminus CYS-6: None > Checking for duplicate atoms > Generating any missing hydrogen atoms and/or adding termini. > Now there are 6 residues with 96 atoms > Making bonds... > Number of bonds was 99, now 98 > Generating angles, dihedrals and pairs... > Before cleaning: 258 pairs > Before cleaning: 258 dihedrals > Keeping all generated dihedrals > Making cmap torsions...There are 258 dihedrals, 21 impropers, 174 angles > 255 pairs, 98 bonds and 0 virtual sites > Total mass 734.892 a.m.u. > Total charge -0.420 e > Writing topology > > Any ideas? > > Extremely thankful > > Sahil > > On 2019-11-28 20:15, Alessandra Villa wrote: > > Hi again, > > On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: > > Hello, > > I am extremely than
Re: [gmx-users] Martini on GROMACS
Hello, All you need to run a Martini simulation is a gro file (most straightforward is to create an atomistic system and use martinize.py or generate lipids by insane.py) and a top file (fairly easy). After that you include the appropriate particle definition itp files in the working directory and you should be good to run grompp. Best wishes, Sahil On 2019-12-03 14:25, Shlomit Afgin wrote: > Hi, > In the tutorial I found only user instructions. > I have GROMACS installed in central place for use of group, I did not find > the installation instruction of Martini into GROMACS installation. > Can someone direct me to the installation instruction? > Thanks > Shlomit > > On 27/11/2019, 15:56, "Justin Lemkul" > jalem...@vt.edu> wrote: > > On 11/27/19 7:15 AM, Shlomit Afgin wrote: >> Hi, >> I installed gromacs 2019.4, I understood it contain MARTINI. >> How can I find MARTINI in gromacs, I just installed? > > Download the MARTINI force field from > http://cgmartini.nl/index.php/downloads and follow the tutorials there. > Preparing the system is somewhat different than for atomistic systems. > GROMACS supports MARTINI but it is not a built-in force field for that > reason. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] amide-capped C-terminus; OPLS force field
Dear all, Does anyone have any experience with capping C-terminal amino acid residues in the OPLS force field? What atomtypes should I use to maintain neutrality of the system? eg. If i have a cystine at the C-terminus residue, and I use the following atomtypes N opls_238 -0.5 H opls_241 0.3 CAopls_224B 0.14 HAopls_140 0.06 CBopls_214 0.0975 HB1 opls_140 0.06 HB2 opls_140 0.06 SGopls_203 -0.2175 C opls_2350.5 O opls_236 -0.5 NTopls_900 -0.9 H1opls_909 0.36 H2opls_909 0.36 The system has a -0.18 qtotal (overall charge). Any help is appreciated. Regards, Sahil -- 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] Disulphide bonded cyclic peptides
Thank you Alessandra. I am extremely grateful for your help. It worked! However, one last bit You suggested to > use the one of the backbone > for your new entry (since you do not have a real termini) for CYS-1 > Nopls_238 -0.500 0 > Hopls_2410.300 0 > CAopls_224B 0.140 1 > > You could also directly change the charges in the top file. Apart from the top file, where could have I specified the opls_X atomtypes? Best regards, Sahil On 2019-11-29 15:46, Alessandra Villa wrote: > Hi, > > On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote: > > Hello, > > Thank you for your suggestions, gave me some insight into my own work. > However, the problem still persists. > > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you have > already H atoms in the pdb I suggest to remove the option -ignh. > > I had already tried removing the -ignh option before posting this here > but did not find success. > > Did you try also without -ter? > > Removing the -ter option does not work in any combination. It always > overrides everything else and breaks the cyclising peptide bond into > NH3+ and COO-. > > . > > Another option could be to remove the extra H from gro/pdb file you got from > pdb2gmx, remove H, (if you want, fix the atom number using editconf), > then try to use the so obtained pdb/gro file as input to pdb2gmx (without > -ter -ignh) > > So this also does not work. pdb2gmx breaks the peptide bond without the > -ter option. > > I tried putting a new entry in the OPLS aminoacids.n.tdb file as you > suggested. I used the opls_910 planar hydrogen for secondary amines as > shown below > > [ CYS2-NH ] > [ replace ] > N opls_900 14.0027 -0.9 > CA opls_912B 12.011 0.12 > [ add ] > 1 1 H N CA C > opls_910 1.008 0.36 > [ delete ] > H You got a charged system, probably because you have generated a new entry without accounting for the partial charge. As atomic charge and atom types I suggest to use the one of the backbone for your new entry (since you do not have a real termini) for CYS-1 Nopls_238 -0.500 0 Hopls_2410.300 0 CAopls_224B 0.140 1 You could also directly change the charges in the top file. I hope this solve the problem Best regards Alessandra Now I can get the peptide bond correctly but the system is charged. > Output below: > > Identified residue CYS1 as a starting terminus. > Identified residue CYS6 as a ending terminus. > 2 out of 2 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS1 CYS1 CYS1 CYS6 CYS6 > N1 C3 SG6 N87 C89 > CYS1 C3 0.244 > CYS1 SG6 0.312 0.419 > CYS6 N87 0.335 0.510 0.486 > CYS6 C89 0.136 0.373 0.322 0.239 > CYS6 SG92 0.387 0.482 0.205 0.420 0.365 > Linking CYS-1 N-1 and CYS-6 C-89... > Linking CYS-1 SG-6 and CYS-6 SG-92... > Select start terminus type for CYS-1 > 0: CYS2-NH > 1: NH3+ > 2: ZWITTERION_NH3+ (only use with zwitterions containing exactly one > residue) > 3: NH2 > 4: None > 0 > Start terminus CYS-1: CYS2-NH > Select end terminus type for CYS-6 > 0: COO- > 1: ZWITTERION_COO- (only use with zwitterions containing exactly one > residue) > 2: COOH > 3: None > 3 > End terminus CYS-6: None > Checking for duplicate atoms > Generating any missing hydrogen atoms and/or adding termini. > Now there are 6 residues with 96 atoms > Making bonds... > Number of bonds was 99, now 98 > Generating angles, dihedrals and pairs... > Before cleaning: 258 pairs > Before cleaning: 258 dihedrals > Keeping all generated dihedrals > Making cmap torsions...There are 258 dihedrals, 21 impropers, 174 angles > 255 pairs, 98 bonds and 0 virtual sites > Total mass 734.892 a.m.u. > Total charge -0.420 e > Writing topology > > Any ideas? > > Extremely thankful > > Sahil > > On 2019-11-28 20:15, Alessandra Villa wrote: > >> Hi again, >> >> On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: >> >> Hello, >> >> I am extremely thankful for your suggestions, but I have a few concerns >> with your advice as stated below. >> >> Hi, >> Below some suggestion that may help you. >> >> On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: >> >> Dear community, >> >> I want to use the OPLS-AA ff to understand the dynamics of a cyclic >> peptide with terminal Cystines that are disulphide linked. To cyclise >> the N- and C- termini, I used a special bond in a specbond.dat file >> placed in my working directory. >> >> 2 >> CYS N 1 CYS C 1 0.14 CYS CYS >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 >> >> and after
Re: [gmx-users] Disulphide bonded cyclic peptides
Hello, Thank you for your suggestions, gave me some insight into my own work. However, the problem still persists. > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you have > already H atoms in the pdb I suggest to remove the option -ignh. I had already tried removing the -ignh option before posting this here but did not find success. Did you try also without -ter? Removing the -ter option does not work in any combination. It always overrides everything else and breaks the cyclising peptide bond into NH3+ and COO-. . > Another option could be to remove the extra H from gro/pdb file you got from > pdb2gmx, remove H, (if you want, fix the atom number using editconf), then > try to use the so obtained pdb/gro file as input to pdb2gmx (without -ter > -ignh) So this also does not work. pdb2gmx breaks the peptide bond without the -ter option. I tried putting a new entry in the OPLS aminoacids.n.tdb file as you suggested. I used the opls_910 planar hydrogen for secondary amines as shown below [ CYS2-NH ] [ replace ] N opls_900 14.0027 -0.9 CA opls_912B 12.011 0.12 [ add ] 1 1 H N CA C opls_910 1.008 0.38 [ delete ] H Now I can get the peptide bond correctly but the system is charged. Output below: Identified residue CYS1 as a starting terminus. Identified residue CYS6 as a ending terminus. 2 out of 2 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS1 CYS1 CYS1 CYS6 CYS6 N1 C3 SG6 N87 C89 CYS1 C3 0.244 CYS1 SG6 0.312 0.419 CYS6 N87 0.335 0.510 0.486 CYS6 C89 0.136 0.373 0.322 0.239 CYS6 SG92 0.387 0.482 0.205 0.420 0.365 Linking CYS-1 N-1 and CYS-6 C-89... Linking CYS-1 SG-6 and CYS-6 SG-92... Select start terminus type for CYS-1 0: CYS2-NH 1: NH3+ 2: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) 3: NH2 4: None 0 Start terminus CYS-1: CYS2-NH Select end terminus type for CYS-6 0: COO- 1: ZWITTERION_COO- (only use with zwitterions containing exactly one residue) 2: COOH 3: None 3 End terminus CYS-6: None Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 6 residues with 96 atoms Making bonds... Number of bonds was 99, now 98 Generating angles, dihedrals and pairs... Before cleaning: 258 pairs Before cleaning: 258 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 258 dihedrals, 21 impropers, 174 angles 255 pairs, 98 bonds and 0 virtual sites Total mass 734.892 a.m.u. Total charge -0.420 e Writing topology Any ideas? Extremely thankful Sahil On 2019-11-28 20:15, Alessandra Villa wrote: > Hi again, > > On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: > > Hello, > > I am extremely thankful for your suggestions, but I have a few concerns > with your advice as stated below. > > Hi, > Below some suggestion that may help you. > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > > Dear community, > > I want to use the OPLS-AA ff to understand the dynamics of a cyclic > peptide with terminal Cystines that are disulphide linked. To cyclise > the N- and C- termini, I used a special bond in a specbond.dat file > placed in my working directory. > > 2 > CYS N 1 CYS C 1 0.14 CYS CYS > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 > > and after the pdb2gmx command I get the following response > > Identified residue CYS2 as a starting terminus. > Identified residue CYS7 as a ending terminus. > 2 out of 2 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS2CYS2CYS2CYS7CYS7 > N1 C3 SG6 N45 C47 > CYS2 C3 0.244 > CYS2 SG6 0.312 0.419 > CYS7 N45 0.335 0.510 0.486 > CYS7 C47 0.136 0.373 0.322 0.239 > CYS7SG50 0.387 0.482 0.205 0.420 0.365 > Linking CYS-2 N-1 and CYS-7 C-47... > Linking CYS-2 SG-6 and CYS-7 SG-50... > > However, the problem arises with the -ter flag in the pdb2gmx command > > pdb2gmx -f in.pdb -o out.gro -ter -ignh > > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you have > already H atoms in the pdb I suggest to remove the option -ignh. I had already tried removing the -ignh option before posting this here but did not find success. Did you try also without -ter? >> In alternative, you could try add a new entry in the file opls force > field > >> file aminoacids.n.tdb for your CYS termini (e.i in place of NH2 put NH). > In > >> alternative you can use the file that you got using NH2 as N-terminus, > and > >> manually remove the extra H you have connected to N (both from top and > gro > >> file). This operation requires to be very careful since you have to > remove > >> the correct H. > > If I remove the extra hydrogen after getting the pdb2gmx ou
Re: [gmx-users] Disulphide bonded cyclic peptides
Hello, I am extremely thankful for your suggestions, but I have a few concerns with your advice as stated below. > Hi, > Below some suggestion that may help you. > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > >> Dear community, >> >> I want to use the OPLS-AA ff to understand the dynamics of a cyclic >> peptide with terminal Cystines that are disulphide linked. To cyclise >> the N- and C- termini, I used a special bond in a specbond.dat file >> placed in my working directory. >> >> 2 >> CYS N 1 CYS C 1 0.14 CYS CYS >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 >> >> and after the pdb2gmx command I get the following response >> >> Identified residue CYS2 as a starting terminus. >> Identified residue CYS7 as a ending terminus. >> 2 out of 2 lines of specbond.dat converted successfully >> Special Atom Distance matrix: >> CYS2CYS2CYS2CYS7CYS7 >> N1 C3 SG6 N45 C47 >> CYS2 C3 0.244 >> CYS2 SG6 0.312 0.419 >> CYS7 N45 0.335 0.510 0.486 >> CYS7 C47 0.136 0.373 0.322 0.239 >> CYS7SG50 0.387 0.482 0.205 0.420 0.365 >> Linking CYS-2 N-1 and CYS-7 C-47... >> Linking CYS-2 SG-6 and CYS-7 SG-50... >> >> However, the problem arises with the -ter flag in the pdb2gmx command >> >> pdb2gmx -f in.pdb -o out.gro -ter -ignh >> >> With the option -ignh, you request pdb2gmx to add H atom. Thus, if you > have already H atoms in the pdb I suggest to remove the option -ignh. I had already tried removing the -ignh option before posting this here but did not find success. > In alternative, you could try add a new entry in the file opls force field > file aminoacids.n.tdb for your CYS termini (e.i in place of NH2 put NH). In > alternative you can use the file that you got using NH2 as N-terminus, and > manually remove the extra H you have connected to N (both from top and gro > file). This operation requires to be very careful since you have to remove > the correct H. If I remove the extra hydrogen after getting the pdb2gmx output, will I not have to edit the topology file also? And will changing the CYS termini in the force field .tdb file not mess with anything else as far as the force field parameters are concerned? Thankful, Sahil > Best regards > Alessandra > >> The output is fine and links the terminal Cystines and putting a disulphide >> bond between them as shown above. But doesn't seem to be >> happy with the -ter command. >> >> Select start terminus type for CYS-2 >> 0: NH3+ >> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one >> residue) >> 2: NH2 >> 3: None >> 3 >> Start terminus CYS-2: None >> Select end terminus type for CYS-7 >> 0: COO- >> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one >> residue) >> 2: COOH >> 3: None >> 3 >> End terminus CYS-7: None >> >> --- >> Program pdb2gmx, VERSION 4.6.7 >> Source code file: >> /home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109 >> >> Fatal error: >> There is a dangling bond at at least one of the terminal ends. Fix your >> coordinate file, add a new terminal database entry (.tdb), or select the >> proper existing terminal entry. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> I cannot understand what is going wrong. The command only works if I >> choose NH2 as my N-terminus, however that in principle violates the >> neutrality of the system. > >> Thanks, >> >> Sahil >> -- -- 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] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide
Dear community, I want to use the OPLS-AA ff to understand the dynamics of a cyclic peptide with terminal-peptide-bonded Cystines that are also disulphide linked (i.e CxxC). To cyclise the N- and C- termini, I used a special bond in a specbond.dat file placed in my working directory. 2 CYS N 1 CYS C 1 0.14 CYS CYS CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 and after the pdb2gmx command I get the following response Identified residue CYS2 as a starting terminus. Identified residue CYS7 as a ending terminus. 2 out of 2 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS2CYS2CYS2CYS7CYS7 N1 C3 SG6 N45 C47 CYS2 C3 0.244 CYS2 SG6 0.312 0.419 CYS7 N45 0.335 0.510 0.486 CYS7 C47 0.136 0.373 0.322 0.239 CYS7SG50 0.387 0.482 0.205 0.420 0.365 Linking CYS-2 N-1 and CYS-7 C-47... Linking CYS-2 SG-6 and CYS-7 SG-50... However, the problem arises with the -ter flag in the pdb2gmx command pdb2gmx -f in.pdb -o out.gro -ter -ignh The output is fine and links the terminal Cystines and putting a disulphide bond between them as shown above. But doesn't seem to be happy with the -ter command. Select start terminus type for CYS-2 0: NH3+ 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) 2: NH2 3: None 3 Start terminus CYS-2: None Select end terminus type for CYS-7 0: COO- 1: ZWITTERION_COO- (only use with zwitterions containing exactly one residue) 2: COOH 3: None 3 End terminus CYS-7: None --- Program pdb2gmx, VERSION 4.6.7 Source code file: /home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I cannot understand what is going wrong. The command only works if I choose NH2 as my N-terminus, however that in-principle violates the valence of the amide N and neutrality of the system. Thanks, Sahil -- 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] Disulphide bonded cyclic peptides
Dear community, I want to use the OPLS-AA ff to understand the dynamics of a cyclic peptide with terminal Cystines that are disulphide linked. To cyclise the N- and C- termini, I used a special bond in a specbond.dat file placed in my working directory. 2 CYS N 1 CYS C 1 0.14 CYS CYS CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 and after the pdb2gmx command I get the following response Identified residue CYS2 as a starting terminus. Identified residue CYS7 as a ending terminus. 2 out of 2 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS2CYS2CYS2CYS7CYS7 N1 C3 SG6 N45 C47 CYS2 C3 0.244 CYS2 SG6 0.312 0.419 CYS7 N45 0.335 0.510 0.486 CYS7 C47 0.136 0.373 0.322 0.239 CYS7SG50 0.387 0.482 0.205 0.420 0.365 Linking CYS-2 N-1 and CYS-7 C-47... Linking CYS-2 SG-6 and CYS-7 SG-50... However, the problem arises with the -ter flag in the pdb2gmx command pdb2gmx -f in.pdb -o out.gro -ter -ignh The output is fine and links the terminal Cystines and putting a disulphide bond between them as shown above. But doesn't seem to be happy with the -ter command. Select start terminus type for CYS-2 0: NH3+ 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue) 2: NH2 3: None 3 Start terminus CYS-2: None Select end terminus type for CYS-7 0: COO- 1: ZWITTERION_COO- (only use with zwitterions containing exactly one residue) 2: COOH 3: None 3 End terminus CYS-7: None --- Program pdb2gmx, VERSION 4.6.7 Source code file: /home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I cannot understand what is going wrong. The command only works if I choose NH2 as my N-terminus, however that in principle violates the neutrality of the system. Thanks, Sahil -- 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.
