Re: [gmx-users] missing of methyl at N-terminal

I have had trouble capping N- and C- terminal residues using the 3.3.X series of GROMACS. I even think I started a thread about it. Before you digg that thread up you should: i) work out what you want to do ii) understand what result you should get iii) do it and check it !!! If that fails I s

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. Terminology is important to get right. You were capping the *C-terminal* end with an *N-methyl*. * i m using forcefield ffgmx. That's a poor idea for anything other than a learning exer

Re: [gmx-users] missing of methyl at N-terminal

hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. * i m using forcefield ffgmx. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as:

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atom

Re: [gmx-users] missing of methyl at N-terminal

thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sortin

Re: [gmx-users] missing of methyl at N-terminal

Bhawana Gupta wrote: hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by

[gmx-users] missing of methyl at N-terminal

hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using pdb2gmx. it give err