subject:"\[gmx\-users\] Nucleotide terminal problems in GORMOS96 force field"

Re: [gmx-users] Nucleotide terminal problems in GORMOS96 force field

2012-10-12 Thread Justin Lemkul

On 10/12/12 2:03 PM, gatidaniel wrote: I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like the this: A02-mdf.top But

[gmx-users] Nucleotide terminal problems in GORMOS96 force field

2012-10-12 Thread gatidaniel

I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like the this: A02-mdf.top But pdb2gmx prompt out such error message: F

Re: [gmx-users] Nucleotide terminal problems in GORMOS96 force field

2012-10-09 Thread Justin Lemkul

On 10/9/12 3:34 AM, 史卜吉 wrote: I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. Gromos96 parameters are rather poor for nucleotides. AMBER or CHARMM parameter sets are far better suited for simulations of nucleic acids. I've bu

[gmx-users] Nucleotide terminal problems in GORMOS96 force field

2012-10-09 Thread 史卜吉

I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like this . But pdb2gmx prompt out such error mess