Re: [gmx-users] select an atom for "only" residue with make_ndx [ Resolved ]
Thanks Justin it worked. For the record, I have also found that 27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33 & rLIPIDC or aC31 | aC32 | aC33 & 27. Note For the two latter commands the order of "r27 or rLIPIDC" is important Thanks again On 5/16/19 5:44 AM, ABEL Stephane wrote: > Thanks Justin > > but it does not work either > > LIPIDC is indeed in a group (#27) > > So I when typed with GMX5.1.4 or GMX2018.2 > > LIPIDC & a C31 | a C32 | a C33 ---> Syntax error: "LIPIDC & a C31 | a C32 | > a C33" > 27 & a C31 | a C32 | a C33 ---> the command works but I selected "all" the > C31, C32 and C33 atoms and not only those in the LIPIDC group Sorry, the correct syntax is: 27 & a C31 C32 C33 -Justin > St?phane > > On 5/15/19 11:03 AM, ABEL Stephane wrote: >> Hello all, >> >> I am currently doing simulations of a model of membranes with different >> types of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a >> group of atoms for only the same lipid with make_ndx. Below an example >> >> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with >> the same name (C31, C32 and C33). With make_ndx I would like to have the >> atoms C33 and C32 for "only" the LIPIDC >> >> So If I do >> >> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 >> lipid types. >> So what is the exact command > Each different [moleculetype] already has its own default group, so > choosing atoms in LIPIDC should be as simple as: > > N & a C31 | a C32 | a C33 > > where N is the group corresponding to LIPIDC. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Message: 5 Date: Thu, 16 May 2019 13:55:33 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Charmm 36m Message-ID: <5a0fe974-b580-dff7-74a3-98ccd6365...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 5/15/19 3:54 PM, Coire Gavin-Hanner wrote: > Dear Gromacs users, > > I am trying to use the charmm36m forcefield to simulate a protein. The most > recent release of charmm36 includes 36m and the ability to toggle between the > two. Is 36m the default state? Yes, though it is possible to use the old C36 parameters with the (hopefully very clear) define statement: define = -DUSE_OLD_C36 Otherwise, the parameters used are C36m. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Message: 6 Date: Thu, 16 May 2019 18:13:34 + (UTC) From: mary ko To: Discussion List for GROMACS Users Subject: [gmx-users] number of coordinates in coordinate file does not match topology Message-ID: <172035957.1411431.1558030414...@mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Hello all I want to run a simulation of a protein from PDB data bank with a ligand. It has two chains and I need only chain A. when I delete chain B in CHIMERA and try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c solve.pdb -p topol.top -o ions.tpr step with the error of number of coordinates in the solve.pdb (143982) does not match the topol.top (143983). I checked the .pdb file and it starts from residue 13. Do I get the error because of that residues not being sorted from 1, since I use the same method for the sorted files and they run without errors.Thank you -- -- 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 181, Issue 39 ** -- 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
Re: [gmx-users] select an atom for "only" residue with make_ndx
On 5/16/19 5:44 AM, ABEL Stephane wrote: Thanks Justin but it does not work either LIPIDC is indeed in a group (#27) So I when typed with GMX5.1.4 or GMX2018.2 LIPIDC & a C31 | a C32 | a C33 ---> Syntax error: "LIPIDC & a C31 | a C32 | a C33" 27 & a C31 | a C32 | a C33 ---> the command works but I selected "all" the C31, C32 and C33 atoms and not only those in the LIPIDC group Sorry, the correct syntax is: 27 & a C31 C32 C33 -Justin Stéphane On 5/15/19 11:03 AM, ABEL Stephane wrote: Hello all, I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of atoms for only the same lipid with make_ndx. Below an example Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 and C32 for "only" the LIPIDC So If I do rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid types. So what is the exact command Each different [moleculetype] already has its own default group, so choosing atoms in LIPIDC should be as simple as: N & a C31 | a C32 | a C33 where N is the group corresponding to LIPIDC. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
[gmx-users] select an atom for "only" residue with make_ndx
Thanks Justin but it does not work either LIPIDC is indeed in a group (#27) So I when typed with GMX5.1.4 or GMX2018.2 LIPIDC & a C31 | a C32 | a C33 ---> Syntax error: "LIPIDC & a C31 | a C32 | a C33" 27 & a C31 | a C32 | a C33 ---> the command works but I selected "all" the C31, C32 and C33 atoms and not only those in the LIPIDC group Stéphane On 5/15/19 11:03 AM, ABEL Stephane wrote: > Hello all, > > I am currently doing simulations of a model of membranes with different types > of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of > atoms for only the same lipid with make_ndx. Below an example > > Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the > same name (C31, C32 and C33). With make_ndx I would like to have the atoms > C33 and C32 for "only" the LIPIDC > > So If I do > > rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 > lipid types. > So what is the exact command Each different [moleculetype] already has its own default group, so choosing atoms in LIPIDC should be as simple as: N & a C31 | a C32 | a C33 where N is the group corresponding to LIPIDC. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] select an atom for "only" residue with make_ndx
On 5/15/19 11:03 AM, ABEL Stephane wrote: Hello all, I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of atoms for only the same lipid with make_ndx. Below an example Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 and C32 for "only" the LIPIDC So If I do rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid types. So what is the exact command Each different [moleculetype] already has its own default group, so choosing atoms in LIPIDC should be as simple as: N & a C31 | a C32 | a C33 where N is the group corresponding to LIPIDC. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
[gmx-users] select an atom for "only" residue with make_ndx
Hello all, I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of atoms for only the same lipid with make_ndx. Below an example Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 and C32 for "only" the LIPIDC So If I do rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid types. So what is the exact command Thanks Stéphane -- 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.
