[gmx-users] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000
Alan
alanwilter at gmail.com
Fri Nov 8 11:04:18 CET 2013
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 <adityasrm027 at 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 C 1 -0.117500 12.01100 ; qtot
> -0.118 CA
> 2 opls_145 1 LIG C1 2 -0.055800 12.01100 ; qtot
> -0.173 CA
> 3 opls_145 1 LIG C2 3 -0.117500 12.01100 ; qtot
> -0.291 CA
> 4 opls_145 1 LIG C3 4 -0.131000 12.01100 ; qtot
> -0.422 CA
> 5 opls_145 1 LIG C4 5 -0.125000 12.01100 ; qtot
> -0.547 CA
> 6 opls_145 1 LIG C5 6 -0.131000 12.01100 ; qtot
> -0.678 CA
> 7 opls_x 1 LIG C6 7 -0.099200 0.00000 ; qtot
> -0.777 x
> 8 opls_x 1 LIG C7 8 -0.105200 0.00000 ; qtot
> -0.882 x
> 9 opls_145 1 LIG C8 9 -0.048800 12.01100 ; qtot
> -0.931 CA
> 10 opls_145 1 LIG C9 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 0.00000 ; qtot
> -1.560 x
> 16 opls_x 1 LIG C15 16 -0.103200 0.00000 ; 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 0.00000 ; qtot
> -2.343 x
> 24 opls_x 1 LIG C23 24 -0.102200 0.00000 ; 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 0.00000 ; qtot
> -3.125 x
> 32 opls_x 1 LIG C31 32 -0.102200 0.00000 ; 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 0.00000 ; qtot
> -3.907 x
> 40 opls_x 1 LIG C39 40 -0.102200 0.00000 ; 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 0.00000 ; qtot
> -4.690 x
> 48 opls_x 1 LIG C47 48 -0.101200 0.00000 ; qtot
> -4.791 x
> --
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--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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