Hi Christoph, if you have a closer look at csgDump_interface, you'll see that masses are always fine, but atom types and residue numbers become messed up in the "List of molecules" section. Line 184 says: 2 Name 3:GLN:CA Type H Mass 12.01 Resnr 2 Resname GLN a clear example of a wrong type. Then, if you move down to line 708, a valine residue has the residue number wrong too. 526 Name 141:VAL:N Type CT Mass 14.01 Resnr 140 Resname VAL 527 Name 142:VAL:H Type HC Mass 1.008 Resnr 141 Resname VAL 528 Name 143:VAL:CA Type HC Mass 12.01 Resnr 142 Resname VAL 529 Name 144:VAL:HA Type C Mass 1.008 Resnr 143 Resname VAL 530 Name 145:VAL:CB Type O Mass 12.01 Resnr 144 Resname VAL 531 Name 146:VAL:HB Type N Mass 1.008 Resnr 145 Resname VAL 532 Name 147:VAL:CG1 Type H Mass 12.01 Resnr 146 Resname VAL 533 Name 148:VAL:HG11 Type H Mass 1.008 Resnr 147 Resname VAL 534 Name 149:VAL:HG12 Type C Mass 1.008 Resnr 148 Resname VAL 535 Name 150:VAL:HG13 Type O Mass 1.008 Resnr 149 Resname VAL 536 Name 151:VAL:CG2 Type N Mass 12.01 Resnr 150 Resname VAL 537 Name 152:VAL:HG21 Type H Mass 1.008 Resnr 151 Resname VAL 538 Name 153:VAL:HG22 Type CT Mass 1.008 Resnr 152 Resname VAL 539 Name 154:VAL:HG23 Type H1 Mass 1.008 Resnr 153 Resname VAL 540 Name 155:VAL:C Type CT Mass 12.01 Resnr 154 Resname VAL 541 Name 156:VAL:O Type HC Mass 16 Resnr 155 Resname VAL
I will try to reproduce the error with a smaller selection of atoms, though I am pretty busy until the 16th Oct. Notes on how to reproduce the error were attached previously, and should not be complicated to follow. I don't know how to interpret the large amount of lines that "gmx dump" prints out, so to check that its output is correct: - you could check that with the previously attached .tpr - I could follow some instructions on how to use "gmx dump". Best, Albert On Sunday, October 1, 2017 at 7:45:10 PM UTC+1, Christoph Junghans wrote: > > Albert, > > 2017-10-01 3:20 GMT-06:00 Albert Solernou <[email protected] > <javascript:>>: > > Hi Cristoph, > > thanks for your reply, and for pointing to the code, and sorry I forgot > to > > attach the messy output. It is now attached, as well as the conflicting > .tpr > > obtained just following the previous notes. > > > > It would be great to know what do you think of it. > Sorry, but what kind of output are you expecting? In your > "csgDump_interface" atomtypes seem to be consistent with the atom > names, same for the masses. > > And have you checked that "gmx dump" outputs the right number? > > Plus, could you make a simple system with just 2 residues exhibit the > same misbehavior? (That would be easier to us to debug.) > > > Christoph > > > > Thanks, > > Albert > > > > > > > > On Friday, September 29, 2017 at 9:58:06 PM UTC+1, Christoph Junghans > wrote: > >> > >> Hi Albert, > >> > >> 2017-09-28 6:24 GMT-06:00 Albert Solernou <[email protected]>: > >> > Hi All, > >> > I think that there is a bug in csg_dump, as it dumps wrong atom types > >> > and > >> > some wrong numbers when working with some modified tpr files. > >> Can you be a bit more explicit which numbers are wrong? > >> > >> > > >> > Not sure how much the bug affects my work, but feel I should report > it > >> > anyway. I attach clear instructions on how to get the bug, as well as > >> > two > >> > input files and the wrong output of the csg_dump. I can send the > whole > >> > set > >> > of files but it is 145M. > >> > > >> > Could you please have a look at this? > >> When csg_dump reads tpr files it uses Gromacs' libgmx, so the first > >> step would be to run "gmx dump" on your tpr files and check if the > >> same "wrong numbers" show up. > >> Honestly VOTCA's wrapper around libgmx is very thin, see: > >> > >> < > https://github.com/votca/csg/blob/master/src/libcsg/modules/io/gmxtopologyreader.cc#L93> > > > >> > >> Christoph > >> > > >> > Many thanks, > >> > Albert > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at https://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
