Dear Justin, Thank you very much.
Best regards, Mijee > > ------------------------------ > > Message: 4 > Date: Mon, 31 Jul 2017 18:47:12 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx mdmat calculation of heavy atoms of two > side chains > Message-ID: <4d68cf73-a92e-85db-1a75-c617ffce3...@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 > > jalem...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Creating Custom .rtp files > Message-ID: <49732a89-48ad-7f19-bc33-ffba2c667...@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.ah...@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 > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > > > > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 160, Issue 1 > ***************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.