Re: [gmx-users] Fatal error:Chain identifier

On 30/12/2010 11:37 PM, ahmet yıldırım wrote: Dear Justin, Firstly, Thanks for your help. You said "You're going from the end of chain B to the beginning of chain A, then back to B later on. Also realize that whatever "ABSG" or "BSG" is." How do you understand it? Where can I find such an im

Re: [gmx-users] Fatal error:Chain identifier

Dear Justin, Firstly, Thanks for your help. You said "You're going from the end of chain B to the beginning of chain A, then back to B later on. Also realize that whatever "ABSG" or "BSG" is." How do you understand it? Where can I find such an important theoretical information? Thanks in advance

Re: [gmx-users] Fatal error:Chain identifier

ahmet yıldırım wrote: OK. if I do what sort change in pdb file, there is no need to create .rtp file. It seems difficult to create the .rtp file. That depends on whether you need this residue, hence all of my previous questions. If there is some functional significance to this residue and

Re: [gmx-users] Fatal error:Chain identifier

OK. if I do what sort change in pdb file, there is no need to create .rtp file. It seems difficult to create the .rtp file. Thanks for your help 29 Aralık 2010 19:49 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> You said "You do not have to make changes in pdb file". >> > >

Re: [gmx-users] Fatal error:Chain identifier

ahmet yıldırım wrote: You said "You do not have to make changes in pdb file". When did I say that? Then How will I create .rtp file. That depends entirely upon what that residue is. Is it a constituent residue of the protein, such that its backbone is incorporated in the protein struct

Re: [gmx-users] Fatal error:Chain identifier

You said "You do not have to make changes in pdb file". Then How will I create .rtp file. 29 Aralık 2010 19:32 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> Thanks for your reply. Where is the error? >> >> Pdb file: >> >> ATOM 1 N ALA A 4 >> ATOM

Re: [gmx-users] Fatal error:Chain identifier

ahmet yıldırım wrote: Dear Justin, Thanks for your reply. Where is the error? Pdb file: ATOM 1 N ALA A 4 ATOM 2 CA ALA A 4 ATOM 2688 N ALA B 4 ATOM 2689 CA ALA B 4 ATOM 5449 OXT GLN B 361 TER5450 GLN B 361 Right here. You're going from

Re: [gmx-users] Fatal error:Chain identifier

Dear Justin, Thanks for your reply. Where is the error? Pdb file: ATOM 1 N ALA A 4 ATOM 2 CA ALA A 4 ATOM 2688 N ALA B 4 ATOM 2689 CA ALA B 4 ATOM 5449 OXT GLN B 361 TER5450 GLN B 361 HETATM 5451 OAAABSG A 1 HETATM 5452 OABABSG A 1

Re: [gmx-users] Fatal error:Chain identifier

ahmet yıldırım wrote: Dear Mark, The chain identifier have continuous. In sequence does not show any problem. Then you're not looking at the right contents; pdb2gmx wouldn't complain otherwise. Usually HETATM entries like HOH (water) are after all protein chains, so you might have chain

Re: [gmx-users] Fatal error:Chain identifier

Dear Mark, The chain identifier have continuous. In sequence does not show any problem. 29 Aralık 2010 15:10 tarihinde Mark Abraham yazdı: > On 29/12/2010 10:12 PM, ahmet yıldırım wrote: > >> Dear users, >> >> a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p >> >> Select the Force

Re: [gmx-users] Fatal error:Chain identifier

On 29/12/2010 10:12 PM, ahmet yıldırım wrote: Dear users, a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p Select the Force Field: 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 710, ato

[gmx-users] Fatal error:Chain identifier

Dear users, a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p Select the Force Field: 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 710, atom 54 49) What should I do to correct this error?