Re: [gmx-users] dna-protein complex simulation

Hi Prasun, I converted it using a script of mine (which unfortunately is not in a shape for shipping yet), and the output file gives me no problem. Looking at it, I notice a difference (do look at it with a fixed-width font): dna.pdb:ATOM 7613 P DTHY I -72 17.935 138.346 27.497 1.00 81

[gmx-users] dna-protein complex simulation

Hello Tsjerk I am attaching a file having a porttion of my PDB file,please check it.Its working for all other nucleotides.There is problem only with DTHY Thanx in advance with regards -- PRASUN (ASHOKA) dna.pdb Description: Protein Databank data ___

Re: [gmx-users] dna-protein complex simulation

Hi Prasun, You probably weren't careful enough when changing the residue names. It seems the residue names need to be shifted by one position, and pdb2gmx reads DTHY as TH somehow, matching it to THF based on the first letters. The proper sed command for the conversion is: sed -e '{s/\(^.\{17\}\

[gmx-users] dna-protein complex simulation

Dear users, I am trying to run a simulation of SNA-protein complex. I have changed DA,DC,DT,DG to DADE,DCYT,DTHY,DGUA and all ' to *. while running the PDB2GMX command, I am getting following error *Program pdb2gmx, VERSION 3.3.2 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom P in resi