[gmx-users] Re: Problem in Disulfide Bond

2011-01-19 Thread parthiban
Hi I am using a dimer for my simulation system which is connected by 2 disulfide bonds. After energy minimization for even few cycles, the disulfide bond breaks which is not expected. i have applied amber99 force field and prepared the system. while i tried with another force field in Gromacs whic

[gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread parthiban
> Message: 5 > Date: Wed, 19 Jan 2011 08:37:20 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > To: Discussion list for GROMACS users > Message-ID: <4d36e910.6030...@vt.edu> > Content-Type: text/plain; charset=ISO

[gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread parthiban
> Message: 3 > Date: Thu, 20 Jan 2011 09:30:00 + > From: Oliver Grant > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Show us t

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-19 Thread Justin A. Lemkul
parthi...@ncbs.res.in wrote: Hi I am using a dimer for my simulation system which is connected by 2 disulfide bonds. After energy minimization for even few cycles, the disulfide bond breaks which is not expected. Bonds do not break in classical molecular mechanics. One of two things is hap

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Oliver Grant
Show us that part of your topology. When you used ffamberports have you renamed the CYS to CYS2? Oliver On 20 January 2011 09:23, wrote: > > Message: 5 > > Date: Wed, 19 Jan 2011 08:37:20 -0500 > > From: "Justin A. Lemkul" > > Subject: Re: [gmx-users] Re

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Mark Abraham
On 01/20/11, parthi...@ncbs.res.in wrote: > > Message: 5 > > Date: Wed, 19 Jan 2011 08:37:20 -0500 > > From: "Justin A. Lemkul" > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users > > Message-ID: &l

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Justin A. Lemkul
parthi...@ncbs.res.in wrote: Message: 3 Date: Thu, 20 Jan 2011 09:30:00 + From: Oliver Grant Subject: Re: [gmx-users] Re: Problem in Disulfide Bond To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Show us that pa

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Mark Abraham
On 01/20/11, parthi...@ncbs.res.in wrote: > > Message: 3 > > Date: Thu, 20 Jan 2011 09:30:00 + > > From: Oliver Grant > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users > > Message-ID: > > 

Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Oliver Grant
In the pdb, before pdb2gmx, rename the CYS residues involved in the S-S bonds as CYS2. If you don't know this then you need to read everything on this page about using the amberports: http://ffamber.cnsm.csulb.edu/ As you may have other issues with HIS and LYS residues. Oliver -- gmx-users mailin