Dear all,
I have a generated .pdb and .str files for copper surface using CHARMM-nanomaterial modeler (http://www.charmm-gui.org/?doc=input/nanomaterial).
This .pdb file can not be used to generate the topology using CHARMM27 in GROMACS as it does not contain the information about copper. But is it possible to convert the .str file to .itp so that it can be further used for the MD calculations?
There is a script on GROMACS website named "convert_charmm_to_gromacs.pl". Can anyone tell me how exactly should I use it in this case?
Thanks in advance.
CHARMM36 supports copper: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
The Perl script to which you refer is designed to convert entire force field files, as I recall, and is almost certainly outdated.
Thanks for the prompt response.
Since I did not find "molname" CU in 'ions.itp' file of CHARMM36, I assumed that copper is absent. But then the question remains - is it possible to convert the .str file to .itp so that it can be further used for the MD calculations?
Earlier I have used CGenFF for the conversion. But in this case, it would not be possible.
I am a new user. Please pardon my naive questions.
Is your surface made of ions? I expected that it would be elemental copper. If you're dealing with ions, you'll have to implement the parameters yourself, not in ions.itp but in the .rtp file so pdb2gmx can generate the topology.
Converting the existing .str to a topology should be possible but there is no generic program/script that will do that. You could modify the CGenFF script to do this, though. You'll still have to add any missing parameters.
Hi Deepashri,
This reference would help you in parametrizing Cu2+ ions in GROMACS simulation.
https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b01122
I am working on elemental copper surface. I am using GROMACS-2019.4.
I tried generating the topology file for the surface using two of the following methods,
Method-1:
========
I generated "topology.top" using pdb2gmx with the help of .pdb that I generated from CHARMM website. For this, I used CHARMM36.
I could generate a .gro file. But I get "segmentation fault" for grompp at energy minimization step. I was using following command,
gmx grompp -f em.mdp -c cu_111_box_updated.gro -p topol.top -o cu_111_emin.tpr
Method-2:
========
Here, I used "par_all36_cgenff.prm", "top_all36_cgenff.rtf" and the .str file for copper surface, generated from CHARMM website. I used a python script availbale on GROMACS website for converting .str to .itp, as follows,
python charmm2gromacs-pvm.py cu_111.str par_all36_cgenff.prm
This gave me: ffbonded.itp, ffnonbonded.itp, forcefield.itp
I copied these in CHARMM36 directory and then generated .gro file. But at grompp step, I get the following error,
ERROR 1 [file ffnonbonded.itp, line 6]:
Atomtype CG301 not found
Attaching my energy minimization file here.
Thanks in advance.
Hi Deepashri Saraf ,
You can use this website http://www.charmm-gui.org/?doc=input/ligandrm to generate necessary CHARMM compatabile .itp files for your system from PDB files and you can use GROMACS for your simulation.
Do lemme know if this helped.
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