[gmx-users] problems with pdb2gmx gromacs 3.3.1 version
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Feb 17 11:18:05 CET 2012
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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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