Re: [gmx-users] disulphide bonds

Hi, The only thing I can think of is that you've run pdb2gmx already and added the termini (adding H1 H2 and H3 for the terminus, which causes the complaints). Now, you're running pdb2gmx for the second time (right?) to merge the chains. Next to -ignh you can also try to simply remove these N-term

Re: [gmx-users] disulphide bonds

Please make sure you're including the gmx-users listserv on your replies. That way, others can weigh in; they may have better ideas than me! So what you're saying, is if you give: "pdb2gmx -f input.pdb -merge" you get the error you mentioned before: Fatal Error: Atom H1 in residue PHE 22 not

Re: [gmx-users] disulphide bonds

rams rams wrote: Hi, If I use -ignh, that will ignore all the hydrogens in my input. And these hydrogens are added by the gromacs.in the first step of creating the top file. What is gromacs.in? Perhaps it would be best if you showed us, step by step, what you are do

Re: [gmx-users] disulphide bonds

Hi, If I use -ignh, that will ignore all the hydrogens in my input. And these hydrogens are added by the gromacs.in the first step of creating the top file. Ram. On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > rams rams wrote: > >> Dear Tsjerk, >> >> Thanks fo

Re: [gmx-users] disulphide bonds

Justin A. Lemkul wrote: rams rams wrote: Hi, The merge command did worked well in creating the disulphide bonds but with that I ran into some other problem. Is there any thing else to add along with the -merge ? Since I have two independent chains, its asking for the n-terminus and c-t

Re: [gmx-users] disulphide bonds

Hi, The merge command did worked well in creating the disulphide bonds but with that I ran into some other problem. Is there any thing else to add along with the -merge ? Since I have two independent chains, its asking for the n-terminus and c-terminus twice. I am giving them as NH3+ and COO- in

Re: [gmx-users] disulphide bonds

rams rams wrote: Dear Tsjerk, Thanks for the suggestion but when I use -merge command it says segmentation error. Let me put the problem in a more elaborated way. I am running this simulation on insulin. It has two chains "a" and "b" which are independent fragments but there are two inter

Re: [gmx-users] disulphide bonds

Dear Tsjerk, Thanks for the suggestion but when I use -merge command it says segmentation error. Let me put the problem in a more elaborated way. I am running this simulation on insulin. It has two chains "a" and "b" which are independent fragments but there are two inter disulphide bonds betwee

Re: [gmx-users] disulphide bonds

Hi Ram, Check the option -merge of pdb2gmx. Cheers, Tsjerk On Thu, Jun 26, 2008 at 6:11 AM, rams rams <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > > Is there any way to handle the disulphide bond formed between two > independent fragments of a protein ? Precisely it is an inter disulphide

[gmx-users] disulphide bonds

Dear Gromacs users, Is there any way to handle the disulphide bond formed between two independent fragments of a protein ? Precisely it is an inter disulphide bond between two fragments. If I keep the two fragments as separate objects while preparing the pdb file (using TER between the two fragmen

Re: [gmx-users] Disulphide bonds

Cesar Araujo wrote: Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? I want to force

[gmx-users] Disulphide bonds

Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? I want to force some disulphide bond a

Re: [gmx-users] Disulphide bonds

Cesar Araujo wrote: Hi, Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option??? it does if they are within the normal distance. are your pdb files ok? Regards, César.- -

Re: [gmx-users] Disulphide bonds

I use the option -merge with my SS-linked peptides, and pdb2gmx always asks me if I want to join my cysteines with a bond. If they're internal to the protein, perhaps it's either that they're too far apart, or you need -ignh as otherwise they've got hydrogens on and potentially can't bond. --- Ce

[gmx-users] Disulphide bonds

Hi,   Anybody knows if there is some way to tell pdb2gmx to recognize automatically S-S bonds and not through the modification of specbond.dat file and -ss option???   Regards, César.-   ---Cesar Araujo, Lic. of ChemistryDepartment of Mo