Re: [gmx-users] Disulphide bonded cyclic peptides

Hello, In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. Yes I figured eventually that it was a stupid question to ask :) Thank you so much. On 2019-12-03 13:44, Alessandra Villa wrote: > Hi > > On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall wrote: > > Thank you Alessandra.

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall wrote: > Thank you Alessandra. > > I am extremely grateful for your help. It worked! > > However, one last bit > > You suggested to > > > use the one of the backbone > > for your new entry (since you do not have a real termini) for CYS-1 > > N

Re: [gmx-users] Disulphide bonded cyclic peptides

Thank you Alessandra. I am extremely grateful for your help. It worked! However, one last bit You suggested to > use the one of the backbone > for your new entry (since you do not have a real termini) for CYS-1 > Nopls_238 -0.500 0 > Hopls_2410.300 0 > CAopls_224B

Re: [gmx-users] Disulphide bonded cyclic peptides

The terminal selection should be NONE. First, you should have a CPN structure with disulfide bonds. https://www.tandfonline.com/doi/abs/10.1080/07391102.2019.1570341 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi, On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote: > Hello, > > Thank you for your suggestions, gave me some insight into my own work. > However, the problem still persists. > > > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you > have already H atoms in the pdb I

Re: [gmx-users] Disulphide bonded cyclic peptides

Hello, Thank you for your suggestions, gave me some insight into my own work. However, the problem still persists. > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you have > already H atoms in the pdb I suggest to remove the option -ignh. I had already tried removing the

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi again, On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: > Hello, > > I am extremely thankful for your suggestions, but I have a few concerns > with your advice as stated below. > > > Hi, > > Below some suggestion that may help you. > > > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote:

Re: [gmx-users] Disulphide bonded cyclic peptides

Hello, I am extremely thankful for your suggestions, but I have a few concerns with your advice as stated below. > Hi, > Below some suggestion that may help you. > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > >> Dear community, >> >> I want to use the OPLS-AA ff to understand the

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi, Below some suggestion that may help you. On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > Dear community, > > I want to use the OPLS-AA ff to understand the dynamics of a cyclic > peptide with terminal Cystines that are disulphide linked. To cyclise > the N- and C- termini, I used a

[gmx-users] Disulphide bonded cyclic peptides

Dear community, I want to use the OPLS-AA ff to understand the dynamics of a cyclic peptide with terminal Cystines that are disulphide linked. To cyclise the N- and C- termini, I used a special bond in a specbond.dat file placed in my working directory. 2 CYS N 1 CYS C 1 0.14 CYS CYS CYS SG 1