Hi, On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall <sl...@ncbs.res.in> 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 N opls_238 -0.500 0 H opls_241 0.300 0 CA opls_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 <sl...@ncbs.res.in> 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 <sl...@ncbs.res.in> 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: > > CYS2 CYS2 CYS2 CYS7 CYS7 > > 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 > > CYS7 SG50 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 output, will I > > not have to edit the topology file also? > > Yes you should fix also the top file, including removing all the > interactions that involve the removed H > > 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) > > > 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? > If properly done, no > > Best regards > Alessandra > > > 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? 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