Hi Cristoph, I am afraid your answer does not fully address the point. See the comments inlined, please.
On Tuesday, October 3, 2017 at 8:34:46 PM UTC+1, Christoph Junghans wrote: > > 2017-10-03 3:45 GMT-06:00 Albert Solernou <[email protected] > <javascript:>>: > > 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 > You can just do: > $ gmx dump -s nvt-100_interface.tpr | less > and look for the atoms block, you will find: > atom[ 2]={type= 2, typeB= 2, ptype= Atom, m= 1.20100e+01, > q=-3.10000e-03, mB= 1.20100e+01, qB=-3.10000e-03, resind= 2, > atomnumber= 6} > That pretty much matches up with the above line, When I said I don't understand "gmx dump", I meant I do not know how you go from here to a PDB line. The error that is showing csg_dump, in the previous line is that 3:GLN:CA is not Type H. That is the most important thing that I think you should look up. > looking in the > "residue" block below: > residue[2]={name="GLN", nr=32, ic=' '} > So the residue name is correct, too. > Yes, the residue name is correct. I always said that it was numbering and atom types. > > The only thing VOTCA does differently is that it start numbering from > 1, while gromacs internally starts with 0, hence "3:GLN:CA" (and not > "2:GLN:CA"). > > > 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 > Again: > atom[ 526]={type= 8, typeB= 8, ptype= Atom, m= 1.40100e+01, > q=-4.15700e-01, mB= 1.40100e+01, qB=-4.15700e-01, resind= 140, > atomnumber= 7} > and > residue[140]={name="VAL", nr=73, ic=' '} > > Do I miss something here? > Yes, here you miss that the residue number goes crazy and that every atom in this region has belongs to a different VAL, while in reality that is not the case. However, I see that this is the numbering that spits "gmx dump", so that should not be your bug, if I understood your comment correctly, Thanks, Albert > Christoph > > > 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]>: > >> > 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]. > >> > 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.
