[gmx-users] the wanging: atom names don't match in top and gro file

[He, Yang]

Hi Mark,

You mean my format in the .GRO file is not very correct. What do you mean by saying " the second column one
too far to the right." ?

Thank you very much.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Tuesday, January 27, 2009 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the wanging: atom names don't match in top and gro     file

He, Yang wrote:
> Hi all users,
>
> when I run the command grompp , it always shows that
>
> processing coordinates...
> Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
>  Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
>  Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> WARNING 1 [file "DNA.top", line 12]:
>   17 non-matching atom names
>   atom names from DNA.top will be used
>   atom names from DNA.gro will be ignored
>
> I have checked that for some times but the warning is still on. I will list the content below:
>  for .GRO FILE
>     1DNA     N10  10   0.668430      0.387405      6.709000
>     1DNA     Q11  11  -5.736999      6.827887      5.566000
>     1DNA     Q12  12   8.266537     -3.346277      4.574000
>     1DNA     C13  13  -1.947247      6.703736      4.660000
>     1DNA     C14  14   5.773899     -3.923511      2.100000
>     1DNA     N15  15   0.161888      0.755429      3.431000
>     1DNA     N16  16   1.506403     -1.802878      3.189000
>     1DNA     Q17  17  -0.627998      8.896000      2.186000
>     1DNA     Q18  18   4.720877     -7.566143      1.194000
>     1DNA     C19  19   2.365001      6.568000      1.280000
>     1DNA     C20  20   2.365001     -6.568000     -1.280000
>     1DNA     N21  21   0.159001      2.344000      0.191000
>     1DNA     N22  22   0.575000     -0.516000     -0.051000

If the .gro format is fixed-format, then you have the second column one
too far to the right.

> FOR itp file
>
>   10    Nda  1     DNA  N10   10       0
>   11    Qa   1     DNA  Q11   11     -1.0
>   12    Qa   1     DNA  Q12   12     -1.0
>   13    C    1     DNA  C13   13       0
>   14    C    1     DNA  C14   14       0
>   15    Nda  1     DNA  N15   15       0
>   16    Nda  1     DNA  N16   16       0
>   17    Qa   1     DNA  Q17   17     -1.0
>   18    Qa   1     DNA  Q18   18     -1.0
>   19    C    1     DNA  C19   19       0
>   20    C    1     DNA  C20   20       0
>   21    Nda  1     DNA  N21   21       0
>   22    Nda  1     DNA  N22   22       0
>
> Any suggestions will be appreciated .
>
> Regards,
>
> Yang
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