[gmx-users] problems with pdb2gmx gromacs 3.3.1 version

francesca vitalini francesca.vitalini11 at gmail.com
Fri Feb 17 11:32:32 CET 2012


Yes I finally got it too. However I've managed to change correctly the
atoms names for the first residue and now it is complaining for the
others. This is my pdb file

ATOM      1  CA  ACE     1      -3.547   1.520   1.054
ATOM      2  H1  ACE     1      -3.081   0.536   0.999
ATOM      3  H2  ACE     1      -3.437   0.016   0.110
ATOM      4  H3  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  HA1 NAC     3       1.413   1.037  -3.050
ATOM     21  HA2 NAC     3       1.506  -0.718  -3.323
ATOM     22  HA3 NAC     3      -0.006   0.155  -3.652

Do you know how to change the other residues or where I can find a
library that has this information?
Thanks


2012/2/17 Mark Abraham <Mark.Abraham at anu.edu.au>:
> On 17/02/2012 9:14 PM, francesca vitalini wrote:
>>
>> 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
>
>
> CH3 is the atom type for the terminal C, CA is its name. I think you have
> misnamed your atoms in your coordinate file.
>
> Mark
>
>
>>
>>
>> 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
>>>
>>> ========================================
>>> --
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>>
>>
>>
>
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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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