[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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