Oh, yes, I could open it in text editor. I didn't realize that. Thanks, Majid
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> Sent: Fri, April 8, 2011 6:48:13 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: > I looked at the error in more detail (output attached), and it says that: >Warning: Residue T6 in chain has different type (Other) from starting residue >A1 >(RNA). I had a dna.pdb file so first but its reading the first residue as RNA. > > So to me, problem seems to be that residues are named differently in my > dna.pdb >file and dna.rtp file of force field. I looked at dna.pdb file using more >dna.pdb (output attached), and the residues are named as A, C, G, T, while in >Amber's dna.rtp file (attached) these are named as DA3, DC3. Could this be a >problem? If this is, then how do I change the names of residues in .pdb file, >which I created it using a different software (3DNA, and Gabedit)? > The names of the residues must conform to the names found in the force field .rtp file. The changes can be made with a text editor, but be careful not to shift the spacing of the .pdb file; its format must remain fixed. -Justin > Thanks, > Majid > >
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