[modeller_usage] Using frcmod+off non-standard residue in modeller.

[Pedro Guillem <>]

Hello,

I'm using Modeller to mutate only. I was wondering how hard it would be to
mutate any position into a non-standard residue. I have my residues in
Amber format (frcmod+off), and I read that I must create the definitions in
CHARMM (RST) format, so modeller understands its topology+charges,etc.

I also have a PDB file and PRMTOP with the non-standard residue. How hard
would it be to make this work in Modeller?. Has anybody done it before?

I see that ParmED (for example) can import the Amber files and generate RST
files from them, but I didn't fully understand how many files I must modify
in modeller, or whether I should use the BLK option, but it is not very
well documented how to do so.

Thanks in advance for any info on this.
Pedro

Hello,

I'm using Modeller to mutate only. I was wondering how hard it would be to mutate any position into a non-standard residue. I have my residues in Amber format (frcmod+off), and I read that I must create the definitions in CHARMM (RST) format, so modeller understands its topology+charges,etc.

I also have a PDB file and PRMTOP with the non-standard residue. How hard would it be to make this work in Modeller?. Has anybody done it before?

I see that ParmED (for example) can import the Amber files and generate RST files from them, but I didn't fully understand how many files I must modify in modeller, or whether I should use the BLK option, but it is not very well documented how to do so.

Thanks in advance for any info on this.
Pedro