2017-10-03 3:45 GMT-06:00 Albert Solernou <[email protected]>:
> 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, looking in the
"residue" block below:
residue[2]={name="GLN", nr=32, ic=' '}
So the residue name is correct, too.
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?
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
>> >> >
>> >> > --
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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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