Re: [gmx-users] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000
Hi, this feature is really really experimental and should indeed be avoided. If opls you want, then give a try with http://www.aribeiro.net.br/mktop/ Alan On 8 November 2013 04:42, aditya sarma adityasrm...@gmail.com wrote: Hi, i was trying to generate topology for p-phenylene vinylene polymer for OPLS forcefield using acpype . The itp file i got has the atomtype opls_x with mass 0.00. Is there any way to rectify this? After reading through how acpype works i found out this was one of the possible errors but there was no solution to it. This is a part of the itp file generated: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_145 1 LIG C1-0.117500 12.01100 ; qtot -0.118 CA 2 opls_145 1 LIGC12-0.055800 12.01100 ; qtot -0.173 CA 3 opls_145 1 LIGC23-0.117500 12.01100 ; qtot -0.291 CA 4 opls_145 1 LIGC34-0.131000 12.01100 ; qtot -0.422 CA 5 opls_145 1 LIGC45-0.125000 12.01100 ; qtot -0.547 CA 6 opls_145 1 LIGC56-0.131000 12.01100 ; qtot -0.678 CA 7 opls_x 1 LIGC67-0.099200 0.0 ; qtot -0.777 x 8 opls_x 1 LIGC78-0.105200 0.0 ; qtot -0.882 x 9 opls_145 1 LIGC89-0.048800 12.01100 ; qtot -0.931 CA 10 opls_145 1 LIGC9 10-0.119500 12.01100 ; qtot -1.051 CA 11 opls_145 1 LIG C10 11-0.118500 12.01100 ; qtot -1.169 CA 12 opls_145 1 LIG C11 12-0.051800 12.01100 ; qtot -1.221 CA 13 opls_145 1 LIG C12 13-0.118500 12.01100 ; qtot -1.339 CA 14 opls_145 1 LIG C13 14-0.119500 12.01100 ; qtot -1.459 CA 15 opls_x 1 LIG C14 15-0.101200 0.0 ; qtot -1.560 x 16 opls_x 1 LIG C15 16-0.103200 0.0 ; qtot -1.663 x 17 opls_145 1 LIG C16 17-0.049800 12.01100 ; qtot -1.713 CA 18 opls_145 1 LIG C17 18-0.119500 12.01100 ; qtot -1.833 CA 19 opls_145 1 LIG C18 19-0.119000 12.01100 ; qtot -1.952 CA 20 opls_145 1 LIG C19 20-0.050800 12.01100 ; qtot -2.002 CA 21 opls_145 1 LIG C20 21-0.119000 12.01100 ; qtot -2.121 CA 22 opls_145 1 LIG C21 22-0.119500 12.01100 ; qtot -2.241 CA 23 opls_x 1 LIG C22 23-0.102200 0.0 ; qtot -2.343 x 24 opls_x 1 LIG C23 24-0.102200 0.0 ; qtot -2.445 x 25 opls_145 1 LIG C24 25-0.050800 12.01100 ; qtot -2.496 CA 26 opls_145 1 LIG C25 26-0.119000 12.01100 ; qtot -2.615 CA 27 opls_145 1 LIG C26 27-0.119000 12.01100 ; qtot -2.734 CA 28 opls_145 1 LIG C27 28-0.050800 12.01100 ; qtot -2.785 CA 29 opls_145 1 LIG C28 29-0.119000 12.01100 ; qtot -2.904 CA 30 opls_145 1 LIG C29 30-0.119000 12.01100 ; qtot -3.023 CA 31 opls_x 1 LIG C30 31-0.102200 0.0 ; qtot -3.125 x 32 opls_x 1 LIG C31 32-0.102200 0.0 ; qtot -3.227 x 33 opls_145 1 LIG C32 33-0.050800 12.01100 ; qtot -3.278 CA 34 opls_145 1 LIG C33 34-0.119000 12.01100 ; qtot -3.397 CA 35 opls_145 1 LIG C34 35-0.119000 12.01100 ; qtot -3.516 CA 36 opls_145 1 LIG C35 36-0.050800 12.01100 ; qtot -3.567 CA 37 opls_145 1 LIG C36 37-0.119000 12.01100 ; qtot -3.686 CA 38 opls_145 1 LIG C37 38-0.119000 12.01100 ; qtot -3.805 CA 39 opls_x 1 LIG C38 39-0.102200 0.0 ; qtot -3.907 x 40 opls_x 1 LIG C39 40-0.102200 0.0 ; qtot -4.009 x 41 opls_145 1 LIG C40 41-0.050800 12.01100 ; qtot -4.060 CA 42 opls_145 1 LIG C41 42-0.119000 12.01100 ; qtot -4.179 CA 43 opls_145 1 LIG C42 43-0.119500 12.01100 ; qtot -4.299 CA 44 opls_145 1 LIG C43 44-0.049800 12.01100 ; qtot -4.348 CA 45 opls_145 1 LIG C44 45-0.119500 12.01100 ; qtot -4.468 CA 46 opls_145 1 LIG C45 46-0.119000 12.01100 ; qtot -4.587 CA 47 opls_x 1 LIG C46 47-0.103200 0.0 ; qtot -4.690 x 48 opls_x 1 LIG C47 48-0.101200 0.0 ; qtot -4.791 x -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the
[gmx-users] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000
Hi, i was trying to generate topology for p-phenylene vinylene polymer for OPLS forcefield using acpype . The itp file i got has the atomtype opls_x with mass 0.00. Is there any way to rectify this? After reading through how acpype works i found out this was one of the possible errors but there was no solution to it. This is a part of the itp file generated: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_145 1 LIG C1-0.117500 12.01100 ; qtot -0.118 CA 2 opls_145 1 LIGC12-0.055800 12.01100 ; qtot -0.173 CA 3 opls_145 1 LIGC23-0.117500 12.01100 ; qtot -0.291 CA 4 opls_145 1 LIGC34-0.131000 12.01100 ; qtot -0.422 CA 5 opls_145 1 LIGC45-0.125000 12.01100 ; qtot -0.547 CA 6 opls_145 1 LIGC56-0.131000 12.01100 ; qtot -0.678 CA 7 opls_x 1 LIGC67-0.099200 0.0 ; qtot -0.777 x 8 opls_x 1 LIGC78-0.105200 0.0 ; qtot -0.882 x 9 opls_145 1 LIGC89-0.048800 12.01100 ; qtot -0.931 CA 10 opls_145 1 LIGC9 10-0.119500 12.01100 ; qtot -1.051 CA 11 opls_145 1 LIG C10 11-0.118500 12.01100 ; qtot -1.169 CA 12 opls_145 1 LIG C11 12-0.051800 12.01100 ; qtot -1.221 CA 13 opls_145 1 LIG C12 13-0.118500 12.01100 ; qtot -1.339 CA 14 opls_145 1 LIG C13 14-0.119500 12.01100 ; qtot -1.459 CA 15 opls_x 1 LIG C14 15-0.101200 0.0 ; qtot -1.560 x 16 opls_x 1 LIG C15 16-0.103200 0.0 ; qtot -1.663 x 17 opls_145 1 LIG C16 17-0.049800 12.01100 ; qtot -1.713 CA 18 opls_145 1 LIG C17 18-0.119500 12.01100 ; qtot -1.833 CA 19 opls_145 1 LIG C18 19-0.119000 12.01100 ; qtot -1.952 CA 20 opls_145 1 LIG C19 20-0.050800 12.01100 ; qtot -2.002 CA 21 opls_145 1 LIG C20 21-0.119000 12.01100 ; qtot -2.121 CA 22 opls_145 1 LIG C21 22-0.119500 12.01100 ; qtot -2.241 CA 23 opls_x 1 LIG C22 23-0.102200 0.0 ; qtot -2.343 x 24 opls_x 1 LIG C23 24-0.102200 0.0 ; qtot -2.445 x 25 opls_145 1 LIG C24 25-0.050800 12.01100 ; qtot -2.496 CA 26 opls_145 1 LIG C25 26-0.119000 12.01100 ; qtot -2.615 CA 27 opls_145 1 LIG C26 27-0.119000 12.01100 ; qtot -2.734 CA 28 opls_145 1 LIG C27 28-0.050800 12.01100 ; qtot -2.785 CA 29 opls_145 1 LIG C28 29-0.119000 12.01100 ; qtot -2.904 CA 30 opls_145 1 LIG C29 30-0.119000 12.01100 ; qtot -3.023 CA 31 opls_x 1 LIG C30 31-0.102200 0.0 ; qtot -3.125 x 32 opls_x 1 LIG C31 32-0.102200 0.0 ; qtot -3.227 x 33 opls_145 1 LIG C32 33-0.050800 12.01100 ; qtot -3.278 CA 34 opls_145 1 LIG C33 34-0.119000 12.01100 ; qtot -3.397 CA 35 opls_145 1 LIG C34 35-0.119000 12.01100 ; qtot -3.516 CA 36 opls_145 1 LIG C35 36-0.050800 12.01100 ; qtot -3.567 CA 37 opls_145 1 LIG C36 37-0.119000 12.01100 ; qtot -3.686 CA 38 opls_145 1 LIG C37 38-0.119000 12.01100 ; qtot -3.805 CA 39 opls_x 1 LIG C38 39-0.102200 0.0 ; qtot -3.907 x 40 opls_x 1 LIG C39 40-0.102200 0.0 ; qtot -4.009 x 41 opls_145 1 LIG C40 41-0.050800 12.01100 ; qtot -4.060 CA 42 opls_145 1 LIG C41 42-0.119000 12.01100 ; qtot -4.179 CA 43 opls_145 1 LIG C42 43-0.119500 12.01100 ; qtot -4.299 CA 44 opls_145 1 LIG C43 44-0.049800 12.01100 ; qtot -4.348 CA 45 opls_145 1 LIG C44 45-0.119500 12.01100 ; qtot -4.468 CA 46 opls_145 1 LIG C45 46-0.119000 12.01100 ; qtot -4.587 CA 47 opls_x 1 LIG C46 47-0.103200 0.0 ; qtot -4.690 x 48 opls_x 1 LIG C47 48-0.101200 0.0 ; qtot -4.791 x -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
