Re: [gmx-users] problem with inflategro
On 3/6/18 9:03 AM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul Thank you very much for your answer, I think input file is correct, when I performed infaltegro again, I found this error Argument C1 isnt numeric in printf at inflategro.pl line 502. Argument C2 isnt numeric in printf at inflategro.pl line 502. Argument C3 isnt numeric in printf at inflategro.pl line 502. Argument N4 isnt numeric in printf at inflategro.pl line 502. Argument C5 isnt numeric in printf at inflategro.pl line 502. Argument C6 isnt numeric in printf at inflategro.pl line 502. Argument O7 isnt numeric in printf at inflategro.pl line 502. Argument P8 isnt numeric in printf at inflategro.pl line 502. Argument O9 isnt numeric in printf at inflategro.pl line 502. Argument C1 isnt numeric in printf at inflategro.pl line 502. Argument C2 isnt numeric in printf at inflategro.pl line 502. Argument C3 isnt numeric in printf at inflategro.pl line 502. Argument N4 isnt numeric in printf at inflategro.pl line 502. Argument C5 isnt numeric in printf at inflategro.pl line 502. Argument C6 isnt numeric in printf at inflategro.pl line 502. Argument O7 isnt numeric in printf at inflategro.pl line 502. Argument P8 isnt numeric in printf at inflategro.pl line 502. Argument O9 isnt numeric in printf at inflategro.pl line 502. I dont know, what is that mean It suggests that your input file is not, in fact, "correct." There is probably some formatting issue somewhere. I suggest adding some debug/print statements to the InflateGRO script to figure out where the problem lies, and inspect the offending lines. -Justin I cant attach my input file because is very large Thank you very much Regards Azadeh -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] problem with inflategro
Hi Dr.Lemkul Thank you very much for your answer, I think input file is correct, when I performed infaltegro again, I found this error Argument C1 isnt numeric in printf at inflategro.pl line 502. Argument C2 isnt numeric in printf at inflategro.pl line 502. Argument C3 isnt numeric in printf at inflategro.pl line 502. Argument N4 isnt numeric in printf at inflategro.pl line 502. Argument C5 isnt numeric in printf at inflategro.pl line 502. Argument C6 isnt numeric in printf at inflategro.pl line 502. Argument O7 isnt numeric in printf at inflategro.pl line 502. Argument P8 isnt numeric in printf at inflategro.pl line 502. Argument O9 isnt numeric in printf at inflategro.pl line 502. Argument C1 isnt numeric in printf at inflategro.pl line 502. Argument C2 isnt numeric in printf at inflategro.pl line 502. Argument C3 isnt numeric in printf at inflategro.pl line 502. Argument N4 isnt numeric in printf at inflategro.pl line 502. Argument C5 isnt numeric in printf at inflategro.pl line 502. Argument C6 isnt numeric in printf at inflategro.pl line 502. Argument O7 isnt numeric in printf at inflategro.pl line 502. Argument P8 isnt numeric in printf at inflategro.pl line 502. Argument O9 isnt numeric in printf at inflategro.pl line 502. I dont know, what is that mean I cant attach my input file because is very large Thank you very much Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- 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] problem with inflategro
On 3/6/18 7:50 AM, kordza...@aut.ac.ir wrote: Hi all when I used inflategro in KALP in DPPC tutorial, I had no problem, but in my system I have a receptor in bilayer , I have 1152 DPPC when I use inflategro in systeminflated.gro file some of lines is duplicated, this happens for 200 DPPC, as follow: 35DPPC 0 1716.798 16.173 4.117 35DPPCC1 1701 20.679 15.409 8.337 35DPPC 01717.798 16.343 4.156 35DPPCC2 1702 20.849 15.448 8.504 35DPPC 01718.798 16.296 4.317 35DPPCC3 1703 20.802 15.609 8.336 35DPPC 01719.798 16.306 4.173 35DPPCN4 1704 20.812 15.465 8.363 what is wrong? what can I do? should I clear copied lines manually? No, you should figure out why this bad formatting occurred. I have never seen the script do anything like this. Is your input .gro file formatted properly? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] problem with inflategro
Hi all when I used inflategro in KALP in DPPC tutorial, I had no problem, but in my system I have a receptor in bilayer , I have 1152 DPPC when I use inflategro in systeminflated.gro file some of lines is duplicated, this happens for 200 DPPC, as follow: 35DPPC 0 1716.798 16.173 4.117 35DPPCC1 1701 20.679 15.409 8.337 35DPPC 01717.798 16.343 4.156 35DPPCC2 1702 20.849 15.448 8.504 35DPPC 01718.798 16.296 4.317 35DPPCC3 1703 20.802 15.609 8.336 35DPPC 01719.798 16.306 4.173 35DPPCN4 1704 20.812 15.465 8.363 what is wrong? what can I do? should I clear copied lines manually? Thanks in advance Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- 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] problem with inflategro
Hi all when I used inflategro in KALP in DPPC tutorial, I had no problem, but in my system I have a receptor in bilayer , I have 1152 DPPC when I use inflategro in systeminflated.gro file some of lines is duplicated, this happens for 200 DPPC, as follow: 35DPPC 0 1716.798 16.173 4.117 35DPPCC1 1701 20.679 15.409 8.337 35DPPC 01717.798 16.343 4.156 35DPPCC2 1702 20.849 15.448 8.504 35DPPC 01718.798 16.296 4.317 35DPPCC3 1703 20.802 15.609 8.336 35DPPC 01719.798 16.306 4.173 35DPPCN4 1704 20.812 15.465 8.363 what is wrong? what can I do? should I clear copied lines manually? Thanks in advance Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- 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] Problem with Inflategro
Hello I am a new user of gromacs. Thanks to Mr Justine Lemkul because of his useful tutorials, Lysozyme in water and kalp15 in DPPC. currently I am practicing kalp15 tutorial in DPPC, and now i have problem with this part: genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 In the .mdp file used for the minimizations, add a line define = - DSTRONG_POSRES to make use of these new position restraints. Then, simply follow the InflateGRO instructions (contained in the script itself), a procedure that is easily scripted. Scale the lipid positions by a factor of 4: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat I did the first command genrestr, but now i have two problems: 1) i cannot find InflateGRO instructions online and i want to know wheather i should do all of its steps or not? and 2) when i have done InflateGRO instructions, i have to execute the second command perl??? thank you very much Razavi -- 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.
