[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
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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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