[gmx-users] Unable to generate .rtp file from gro and pdb file.

Mark Abraham mark.j.abraham at gmail.com
Sun Nov 11 08:27:42 CET 2018


Hi,

Does your input conformation + topology work for a single molecule of this
type?

Mark

On Sun, Nov 11, 2018 at 1:08 AM Karpurmanjari Kakati <
ch18resch01002 at iith.ac.in> wrote:

> Hi
> I tried doing the same, like you said.
> 1. Copied the OPLS AA force field files to the directory, where my pdb
> files were present.
> 2. Modified the rtp file. but the error comes up in the pdb2gmx "no
> residjue type in the residue database. "
> Alternatively, what I tired doing is the following:
>
> 1. I constructed the polymer in Avogrado software.
> 2. Used OBGMX to make the itp file. But the charge column genereated by
> OBGMX is 0000.
> 3. To include charge, I went back to Avogrado, and took the charges from
> each atom and included it in the itp file by replacing the 0000  against
> each atom.
> 4. Now my topology file looks something like this:
>
>
>
> #include "oplsaa.ff/forcefield.itp"
>
>
>
> [ atomtypes ]
> ; name1 name2   mass     charge  ptype   sigma   epsilon
> N_3      N_3        14.0067      0.227    A      0.3261       0.2889
> C_3      C_3        12.0107      0.050   A      0.3431       0.4396
> C_2      C_2        12.0107      0.261  A      0.3431       0.4396
> O_2      O_2        15.9994      -0.013   A      0.3118       0.2512
> N_2      N_2        14.0067      -0.302   A      0.3261       0.2889
> N_R      N_R        14.0067      -0.289   A      0.3261       0.2889
> O_3      O_3        15.9994      -0.390    A      0.3118       0.2512
> H_       H_          1.0079      0.200  A      0.2571       0.1842
> NE      NE        14.0067      0.227   A      0.3261       0.2889
> NH1      NH1        14.0067      0.227   A      0.3261       0.2889
> NH2      NH2        14.0067      0.227   A      0.3261       0.2889
>
> CA      CA        12.0107      0.050   A      0.3431       0.4396
> C      C        12.0107      0.050  A      0.3431       0.4396
> CB      CB        12.0107      0.261   A      0.3431       0.4396
> CG      CG        12.0107      0.261   A      0.3431       0.4396
> CD      CD        12.0107     0.261   A      0.3431       0.4396
> CZ      CZ        12.0107      0.261   A      0.3431       0.4396
> N       N        14.0067      0.227    A      0.3261       0.2889
> H1       H1          1.0079      0.200   A      0.2571       0.1842
> H2       H2          1.0079      0.200   A      0.2571       0.1842
> HA       HA          1.0079     0.200   A      0.2571       0.1842
> HB1       HB1          1.0079      0.200   A      0.2571       0.1842
> HB2       HB2          1.0079      0.200   A      0.2571       0.1842
> HB3       HB3          1.0079      0.200   A      0.2571       0.1842
> H       H          1.0079      0.200   A      0.2571       0.1842
> HA1       HA1          1.0079      0.200   A      0.2571       0.1842
> HA2       HA2          1.0079      0.200   A      0.2571       0.1842
> HG1       HG1          1.0079      0.200   A      0.2571       0.1842
> HG2       HG2          1.0079      0.200   A      0.2571       0.1842
> HD1       HD1          1.0079      0.200   A      0.2571       0.1842
> HD2       HD2          1.0079      0.200   A      0.2571       0.1842
> HE       HE          1.0079      0.200   A      0.2571       0.1842
> HH21       HH21          1.0079      0.200   A      0.2571       0.1842
> HH22       HH22          1.0079      0.200   A      0.2571       0.1842
> HH11       HH11          1.0079      0.200   A      0.2571       0.1842
> HH12       HH12          1.0079      0.200   A      0.2571       0.1842
> HG       HG          1.0079      0.200   A      0.2571       0.1842
> HD       HD          1.0079      0.200   A      0.2571       0.1842
> HW1       HW1          1.0079     0.200   A      0.2571       0.1842
> HW2      HW2          1.0079      0.200   A      0.2571       0.1842
> O      O        15.9994     -0.390   A      0.3118       0.2512
>
>
>
> #include <ge.itp>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre-gel.itp"
> #endif
>
> #include <peg.itp>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre-pe.itp"
> #endif
>
> [ system ]
> GEL and PE
>
> [ molecules ]
> GEL      5
> PE       2
>
>
>
> And now I am performing EM in vacuum for the system. The error comes to be
> it stops Energy minimization before the desired energy is reached.
> Like I read from other error mails, it says the topology or the itp file
> had defects.
>
>
> My query is, I just added charges to the itp file generated from OBGMX.
> Is that the reason why my energy minimization is stopping at the middle.
>
> Kindly help with this.
>
>
> Karpurmanjari
>
>
>
>
>
>
>
>
>
>
> On Mon, Nov 5, 2018 at 10:46 PM Karpurmanjari Kakati <
> ch18resch01002 at iith.ac.in> wrote:
>
> > Dear Justin,
> >
> > I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the
> > aminoacids.rtp file . I have all the files of OPLS AA force field in my
> > working directory.
> > For that I tried to generate the initial rtp format file from the hydroxy
> > proline's .pdb and .gro  files using the following command:
> > gmx x2top  -f hyd.gro  -r hyd.rtp  -pbc -ff oplsaa
> >
> > and I got the following error:
> >
> > Opening force field file
> /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t
> > There are 23 name to type translations in file oplsaa.ff
> > Generating bonds from distances...
> > atom 18
> > Can not find forcefield for atom CA-2 with 4 bonds
> > Can not find forcefield for atom C-3 with 3 bonds
> > Can not find forcefield for atom CD-7 with 4 bonds
> >
> > -------------------------------------------------------
> > Program:     gmx x2top, version 2018.1
> > Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 205)
> >
> > Fatal error:
> > Could only find a forcefield type for 15 out of 18 atoms.
> >
> >
> > Can you help me with this.
> >
> > I want to add this residue to the rtp file so that I can use the step
> > pdb2gmx directly.
> >
> >
> > Aijoni
> >
> >
> >
> >
> --
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