Albert,
2017-10-13 3:50 GMT-06:00 Albert Solernou <a.soler...@gmail.com>:
> 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 <a.sol...@gmail.com>:
>> > 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.
Ok, I see what you mean!
VOTCA's identifier scheme is <resnr>:<resname>:<atomname>, so the last
part is the atomname not the atomtype. Atomtypes would make for a
unique identifier string.
However look again at the output of "gmx dump" I see:
atom[2]={name="CA"}
So VOTCA basically just picks up the name from inside the tpr, which
is obviously the wrong name, but there isn't much we can do about
that.
>
>>
>> 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,
Yeah I would ask on the gmx developer list
(gmx-develop...@gromacs.org) about this odd behavior. It seems to me
something in your pre-processing went wrong.
Christoph
>
>
> 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 <a.sol...@gmail.com>:
>> >> > 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 <a.sol...@gmail.com>:
>> >> >> > 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
>> >> >> >
>> >> >> > --
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>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
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>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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