[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

francesca vitalini francesca.vitalini11 at gmail.com
Fri Feb 17 11:14:22 CET 2012


I tried, but apparently the atom that it is looking for exist already
in the rtp file!!

this is the error

Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2gmx.c, line: 383

Fatal error:
Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms
             while sorting atoms


and this is the rtp file for residue ACE

[ ACE ]
 [ atoms ]
    CA   CH3   0.000     0
     C     C   0.450     1
     O     O  -0.450     1
 [ bonds ]
     C    CA   gb_27
     C     O   gb_5
     C    +N   gb_19
 [ angles ]
   CA     C    +N    ga_19
    O     C    +N    ga_33
 [ impropers ]
    C    CA    +N     O    gi_1

[ NH2 ]
 [ atoms ]
     N    NT   -0.83    0
     H1    H   0.415    0
     H2    H   0.415    0
[ bonds ]
      N    H1  gb_2
      N    H2  gb_2
     -C    N   gb_9
 [ angles ]
     -O -C N  ga_33
     -CA -C N ga_19
     -C N H1  ga_23
     -C N H2  ga_23
     H1 N H2  ga_24
 [ dihedrals ]
    -CA -C N H1 gd_14
 [ impropers ]
    -C -O N -CA gi_1
     N  H H  -C gi_1


Any help?



2012/2/16 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> francesca vitalini wrote:
>>
>> Do you mean that I can just use the new version of pdb2gmx than change
>> the included forcefield and in case the name of the atoms and it
>> should work?
>>
>
> You still have to fix the incorrect atom name(s), regardless of version.
>  You can use a new version to make use of pdb2gmx -ter, if necessary.
>  Otherwise, your version should work for what you need.
>
> -Justin
>
>
>>
>> 2012/2/16 Justin A. Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>> francesca vitalini wrote:
>>>>
>>>> Hi all!
>>>> I'm trying to create a topology file from the pdb using the pdb2gmx
>>>> command of gromacs 3.3.1 but I'm encountering some issues. I should
>>>> use the flag -tar in order to select interactively the termini, but
>>>> with the old version of gromacs this is not implemented and I cannot
>>>> use a new one because I need the reverse transformation tool which is
>>>> only implemented in that version.
>>>
>>>
>>> The topology format is largely unaffected by differences in version.  A
>>> few
>>> moments with a text editor to fix the #include statements written by a
>>> version in the 4.5.x series would solve any problems.
>>>
>>>
>>>> Here it is the pdb I'm using
>>>>
>>>> REMARK
>>>> ATOM      1 1HH3 ACE     1      -3.547   1.520   1.054
>>>> ATOM      2  CH3 ACE     1      -3.081   0.536   0.999
>>>> ATOM      3 2HH3 ACE     1      -3.437   0.016   0.110
>>>> ATOM      4 3HH3 ACE     1      -3.348  -0.041   1.883
>>>> ATOM      5  C   ACE     1      -1.570   0.683   0.929
>>>> ATOM      6  O   ACE     1      -1.051   1.800   0.938
>>>> ATOM      7  N   ALA     2      -0.862  -0.446   0.851
>>>> ATOM      8  H   ALA     2      -1.368  -1.322   0.859
>>>> ATOM      9  CA  ALA     2       0.607  -0.509   0.828
>>>> ATOM     10  HA  ALA     2       0.997   0.272   1.484
>>>> ATOM     11  CB  ALA     2       1.025  -1.867   1.412
>>>> ATOM     12 1HB  ALA     2       2.113  -1.918   1.485
>>>> ATOM     13 2HB  ALA     2       0.676  -2.677   0.770
>>>> ATOM     14 3HB  ALA     2       0.604  -1.990   2.411
>>>> ATOM     15  C   ALA     2       1.238  -0.262  -0.565
>>>> ATOM     16  O   ALA     2       2.465  -0.181  -0.678
>>>> ATOM     17  N   NAC     3       0.423  -0.139  -1.620
>>>> ATOM     18  H   NAC     3      -0.569  -0.212  -1.447
>>>> ATOM     19  CH3 NAC     3       0.860   0.098  -2.992
>>>> ATOM     20 1HH3 NAC     3       1.413   1.037  -3.050
>>>> ATOM     21 2HH3 NAC     3       1.506  -0.718  -3.323
>>>> ATOM     22 3HH3 NAC     3      -0.006   0.155  -3.652
>>>> TER
>>>> END
>>>>
>>>>
>>>> And this is the pdb2gmx command
>>>> path/pdb2gmx -ignh -missing -f struct1-1.pdb -p ala.top -o ala.gro
>>>>
>>>>
>>>> I use the gromos9653a6 forcefield and the spc water model
>>>>
>>>> And this is the error I get
>>>>
>>>> There are 2 donors and 2 acceptors
>>>> There are 2 hydrogen bonds
>>>> -------------------------------------------------------
>>>> Program pdb2gmx, VERSION 3.3.1
>>>> Source code file: pdb2gmx.c, line: 383
>>>>
>>>> Fatal error:
>>>> Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms
>>>>            while sorting atoms
>>>> -------------------------------------------------------
>>>>
>>>> Any suggestions?
>>>
>>>
>>> Check the .rtp file - your atom is named in a way that is inconsistent
>>> with
>>> what the force field expects.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
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>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> or send it to gmx-users-request at gromacs.org.
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-- 
Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412



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