How to add a new termini database entries in amber FF for phosphorylated at 5'- and 3'-termini of DNA?
Pdb2gmx is not able to covert pdb to gro files
could you please help me?
You could use editconf command to convert .pdb file to .gro file or .gro to .pdb
gmx editconf -f file.pdb -o file.gro
or
gmx editconf -f file.gro -o file.pdb
Azadeh Kordzadeh Anwesh Pandey the problem is not in the command itself , but most FFs dont support the phosphorelated terminal in DNA . So we need to add .tdp entry to account for DNA terminals. Do you have any idea about that?
thank you very much.
Try this and let me know:
gmx pdb2gmx -f dna.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp
Anwesh Pandey Thank you very much for your response. the problem is the recommended FF is amber FF. Do you know how to parametrize the FF to make it able to support the phosphorylated terminal of DNA?
In the previous commamd just skip the -ff flag and charmm27 and run the remaining command, it will automatically ask for the choice of ff then select the one which you prefer.
i.e.,
gmx pdb2gmx -f dna.pdb -water tip3p -ignh -o conf.pdb -nochargegrp
See this paper, this might help:
https://scholar.google.com/citations?hl=en&user=MEGYE_UAAAAJ&view_op=list_works&sortby=pubdate#d=gs_md_cita-d&u=%2Fcitations%3Fview_op%3Dview_citation%26hl%3Den%26user%3DMEGYE_UAAAAJ%26sortby%3Dpubdate%26citation_for_view%3DMEGYE_UAAAAJ%3AtkaPQYYpVKoC%26tzom%3D-330
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