Re: [gmx-users] Capping residues

2010-07-07 Thread Justin A. Lemkul
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Re: [gmx-users] Capping residues

2010-07-07 Thread Justin A. Lemkul
<mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>

Re: [gmx-users] Capping residues

2010-07-07 Thread Justin A. Lemkul
ail.com <mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>> <mailto:saipo...@gmail.com

Re: [gmx-users] Capping residues

2010-07-07 Thread Sai Pooja
u choosing as your termini when running >>pdb2gmx? It >> should be "none," since by capping, you are not choosing a >> protonation state for the N- and C-termini. >> >> -Justin >> >&g

Re: [gmx-users] Capping residues

2010-07-07 Thread Justin A. Lemkul
<mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>>>

Re: [gmx-users] Capping residues

2010-07-07 Thread Sai Pooja
What are you choosing as your termini when running pdb2gmx? It >>should be "none," since by capping, you are not choosing a >>protonation state for the N- and C-termini. >> >>-Justin >> >> >> Pooja >> >>

Re: [gmx-users] Capping residues

2010-07-03 Thread Justin A. Lemkul
aipo...@gmail.com>>> Date: Friday, July 2, 2010 7:28 Subject: Re: [gmx-users] Capping residues To: jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>, Discussion lis

Re: [gmx-users] Capping residues

2010-07-03 Thread Sai Pooja
;> "none," since by capping, you are not choosing a protonation state for the >> N- and C-termini. >> >> -Justin >> >> >>> Pooja >>> >>> >>> >>> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham >>> >> mark.

Re: [gmx-users] Capping residues

2010-07-02 Thread Sai Pooja
by capping, you are not choosing a protonation state for the > N- and C-termini. > > -Justin > > >> Pooja >> >> >> >> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham >> > mark.abra...@anu.edu.au>> wrote: >> >> >> &g

Re: [gmx-users] Capping residues

2010-07-02 Thread Justin A. Lemkul
lto:mark.abra...@anu.edu.au>> wrote: - Original Message - From: Sai Pooja mailto:saipo...@gmail.com>> Date: Friday, July 2, 2010 7:28 Subject: Re: [gmx-users] Capping residues To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for GROMACS use

Re: [gmx-users] Capping residues

2010-07-02 Thread Sai Pooja
aminoacids.n.tdb file as well? Pooja On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham wrote: > > > - Original Message - > From: Sai Pooja > Date: Friday, July 2, 2010 7:28 > Subject: Re: [gmx-users] Capping residues > To: jalem...@vt.edu, Discussion list for GROMACS users <

Re: [gmx-users] Capping residues

2010-07-01 Thread Mark Abraham
- Original Message - From: Sai Pooja Date: Friday, July 2, 2010 7:28 Subject: Re: [gmx-users] Capping residues To: jalem...@vt.edu, Discussion list for GROMACS users > I am sorry if I did not frame the question correctly, but putting it very > simply, is there a way to use c

Re: [gmx-users] Capping residues

2010-07-01 Thread Sai Pooja
I am sorry if I did not frame the question correctly, but putting it very simply, is there a way to use capping residues with the charmm forcefield if the residues are --COCH3 and NHCH3? On Thu, Jul 1, 2010 at 4:58 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > >> Would it be possible to a

Re: [gmx-users] Capping residues

2010-07-01 Thread Justin A. Lemkul
Sai Pooja wrote: Would it be possible to add some capping residues (like --COCH3 and --NHCH3) by writing a separate .itp file and including it in the topology file? Is there a way to make it consistent with charmm forcefield? No, because you have to specify bonds between these capping resi

Re: [gmx-users] Capping residues

2010-07-01 Thread Sai Pooja
must one do before using these .rtp files? On Wed, Jun 30, 2010 at 8:39 PM, Mark Abraham wrote: > > > - Original Message - > From: "Justin A. Lemkul" > Date: Thursday, July 1, 2010 9:58 > Subject: Re: [gmx-users] Capping residues > To: Discussion list for G

Re: [gmx-users] Capping residues

2010-06-30 Thread Mark Abraham
- Original Message - From: "Justin A. Lemkul" Date: Thursday, July 1, 2010 9:58 Subject: Re: [gmx-users] Capping residues To: Discussion list for GROMACS users > > > Sai Pooja wrote: > >Hi, > > > >1) What capping residues are recognized by ch

Re: [gmx-users] Capping residues

2010-06-30 Thread Justin A. Lemkul
Sai Pooja wrote: Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? It looks like there aren't any. Check the .rtp file to be sure. I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define c

[gmx-users] Capping residues

2010-06-30 Thread Sai Pooja
Hi, 1) What capping residues are recognized by charmm implemented on gromacs in the latest git version? I was trying to use ACE for acetyl but it is not recognized by pdb2gmx. 2) Is it possible to define caps at residues other than those at the termini? Regards Pooja -- Quaerendo Invenietis-S