Hi

On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall <sl...@ncbs.res.in> 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
> > 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.
>
> 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 <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
> >> --
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