[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

>> Would you be willing to share the exact sequence of events, commands, etc. >> that worked? OK, Consider that the Atosiban cyclic peptide (https://fr.wikipedia.org/wiki/Atosiban) with 2 custom residues (3-Mercaptopropionyl, MEr) and ethyloxyde TYR (TYO) at Nter. The Mer is bonded to the

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

On 1/15/18 12:31 PM, ABEL Stephane wrote: Hello, I have finally resolved my problem thank to Justin . Would you be willing to share the exact sequence of events, commands, etc. that worked? As I mentioned before, these threads often trail off or end unresolved, so while it is nice that

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

Hello, I have finally resolved my problem thank to Justin . Bye -- Message: 2 Date: Sun, 14 Jan 2018 17:36:21 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem fpr building a peptide with two modified

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

On 1/14/18 12:04 PM, ABEL Stephane wrote: Thank you, Justin for your interest to my problem, But even if I use the -missing argument*, pdb2gmx still wants to add an Nter ILE instead of a central a simple ILE :(( Ile should not be treated as a terminal residue, and it wasn't in the screen

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Thank you, Justin for your interest to my problem, But even if I use the -missing argument*, pdb2gmx still wants to add an Nter ILE instead of a central a simple ILE :(( *gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

-- Stéphane Abel, Ph.D. Commissariat à l’Energie Atomique et aux Energies Alternatives Centre de Saclay DSV/ISVFJ/SB2SM Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

On 1/14/18 10:04 AM, ABEL Stephane wrote: Hi Justin I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6 ## gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Hi Justin I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6 ## gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes Select

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

On 1/14/18 9:23 AM, ABEL Stephane wrote: Dear all, I have a peptide with two modified residues at the Nter with the following sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified tyrosine residue (side chain), respectively. the Mer, TYR and ILE are bonded together

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Dear all, I have a peptide with two modified residues at the Nter with the following sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified tyrosine residue (side chain), respectively. the Mer, TYR and ILE are bonded together with a peptide bond. To build the corresponding