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

[Karpurmanjari Kakati]

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
>>
>>
>>
>>