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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