i am doing this simulation with martini coarse grained force field. so i just replace p and n by bead name and it is working now. thank you so much again for your reply.
On Wed, Oct 30, 2019 at 1:04 PM SHAHEE ISLAM <islamsha...@gmail.com> wrote: > i am so sorry for the late reply. I have applied both of your suggestion > but still it does not working. > syntax error > invalid selection 'POPG and name P* N* within 1.0 of Protein' > can you please guide me to solve the error. > > On Fri, Oct 25, 2019 at 3:39 PM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 10/25/19 5:38 AM, Peter Stern wrote: >> > You are probably causing your command to run in the background with >> “&”. Try using “and” instead. >> >> In addition to this, the selection string needs to be enclosed by single >> quotes. >> >> -Justin >> >> > Peter >> > >> > Sent from my iPhone >> > >> >> On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM <islamsha...@gmail.com> >> wrote: >> >> >> >> Hi, >> >> I am trying to calculate the angle between P and N vector of my lipid >> >> (popc+popg) with regards to the z axis to see how the protein is >> affecting >> >> the membrane. I am using this command, but it does not working >> >> gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of >> >> Protein -oi number.dat >> >> but the problem is, when the command is running only >> >> gmx select -f *.xtc -s *.tpr -select POPG >> >> this command. >> >> Can anyone please guide me what i am doing wrong. >> >> Thanking you >> >> Shahee >> >> -- >> >> 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. >> 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. > > -- 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.
