[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 1

[Мижээ Батсайхан]

Dear Justin,

Thank you very much.

Best regards,

Mijee

>
> ------------------------------
>
> Message: 4
> Date: Mon, 31 Jul 2017 18:47:12 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx mdmat calculation of heavy atoms of two
>         side chains
> Message-ID: <4d68cf73-a92e-85db-1a75-c617ffce381a at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 7/31/17 1:19 AM, ????? ????????? wrote:
> > Dear gmx users,
> >
> > I would like to know about the hydrophobic interaction between heavy
> atoms
> > of side chains in different chains of peptides. How can I use mdmat tool
> > for this calculation? I  separately indexed all heavy atoms but mdmat use
> > only one index group in the calculation. I re-integrated all separate
> > groups into a group. Calculation result came out only two side chain
> > distance image.
>
> A single, merged group is the proper approach.  This is the only way to
> get a
> matrix of all (NxN) atomic interactions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 31 Jul 2017 18:48:52 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Creating Custom .rtp files
> Message-ID: <49732a89-48ad-7f19-bc33-ffba2c667d14 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 7/31/17 7:47 AM, Momin Ahmad wrote:
> > Hello,
> >
> > the .rtp file is located in the same directory as the force-field. When
> i type
> > gmx gmx2pdb ..... then the log shows that the right path is considered
> and loads
> > the needed .rtp fiels that already exist in the forc-field file. But my
> custom
> > one is ignored.
> >
>
> Please post the full screen output of pdb2gmx, including the force field
> selection.  If your .rtp file is not being read, it is likely
> misformatted, in
> which case you should either write your new residue entries in an existing
> file
> or upload it to a file-sharing service so we can provide feedback.
>
> -Justin
>
> > Greets
> > Momin Ahmad
> >
> > Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:
> >> On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad <momin.ahmad at kit.edu>
> wrote:
> >>
> >>> Hi,
> >>>
> >>> I created a custom .pdb file and the associated .rtp file for the
> >>> force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the
> >>> 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
> >>> version is a local installation in my /home/user folder. The log shows
> >>> the correct paths but does not consider my custom .rtp file.
> >> I would recommend to check whether the rtp file location and source
> where
> >> gmx  you have installed match. Apart from that I do not think any error
> >> with version of Gromacs.
> >>
> >>> Am i doing
> >>> something wrong with the newer version? I added two simple files of my
> >>> problem. Thanks in advance.
> >>>
> >>> Cheers
> >>> Momin Ahmad
> >>> Karlsruher Institut of Technology
> >>> Germany
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>> posting!
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> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
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> End of gromacs.org_gmx-users Digest, Vol 160, Issue 1
> *****************************************************
>