[gmx-users] the wanging: atom names don't match in top and gro file
Justin A. Lemkul
jalemkul at vt.edu
Wed Jan 28 03:19:52 CET 2009
He, Yang wrote:
> 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." ?
>
Yes, your structure file seems mangled. For .gro format specifications:
http://www.gromacs.org/documentation/reference_4.0/online/gro.html
-Justin
> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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