[gmx-users] Translating .frcmod and .prep to .itp
fanc232 at nenu.edu.cn
Thu Jul 2 13:39:58 CEST 2015
I wish I could offer some help. <br/>I used to prepare small compound molecules, and the ligand.frcmod was generated by parmchk of AMBER. The ligand.frcmod was then handed to tleap or xleap of AMBER, to generate ligand.prmtop and ligand.inpcrd. Following that, a python script called "acpype.py" was employed to generate gromacs topology files, and the command is like this:<br/><br/>$python2.7 acpype.py -p ligand.prmtop -x ligand.inpcrd<br/><br/>Then you could find the gromacs structure file ending with .gro and the topology file with .top . However, there're some differences between .top and .itp file. You have to make some changes by hand, such as deleting the first few lines and the ending line of the .top file, to transfer it to a .itp file.
At 2015-07-02 19:16:57, Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:
>I have parameters for 8-oxoguanine in FRCMOD and PREP files. Adding
>information from .prep file to dna.rtp an creating a modified entry in
>dna.hdb is simple enough.
>However I'm stuck now translating bond and angle data from .frcmod to
>.itp file, as its notation system is very different and its GROMACS
>manual section (5.3.3) lacks any substantial description of its formatting.
>Is there any scripts or howtos for this, or at least a more detailed
>description for ffbonded.itp?
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