[gmx-users] Unable to generate .rtp file from gro and pdb file.
Mark Abraham
mark.j.abraham at gmail.com
Wed Nov 14 05:29:28 CET 2018
Hi,
Your topology had 5 GEL and 2 PE, which means you have 7 things that could
be a problem. Start with 1 so you find out where the problem is.
Mark
On Mon, Nov 12, 2018 at 10:40 PM Karpurmanjari Kakati <
ch18resch01002 at iith.ac.in> wrote:
> Hi,
> I didn't understand, what you exactly meant. Could you be more elaborate?
>
> Karpurmanjari
>
> On Sun, Nov 11, 2018 at 12:37 PM 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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