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

[Karpurmanjari Kakati]

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
>
>
>
>