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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php