[gmx-users] Topology file-residue unknown
Juliette N.
joojoojooon at gmail.com
Fri Apr 5 00:17:22 CEST 2013
Hi Justin,
Thanks a lot for your message. I am petrified why pdb2gmx is not
recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
but as you may see below it is not read from rtp.
I am sure this residue is added to ffoplsaa.rtp which is existing in the
working directory:
[ ETY ]
[ atoms ]
C1 opls_143 -0.120 1
H11 opls_144 0.060 1
H12 opls_144 0.060 1
C2 opls_143 -0.120 2
H21 opls_144 0.060 2
H22 opls_144 0.060 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
;C2 C1
Then I issue:
pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 4.5.4 (-:
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP3P TIP 3-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
6
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading Ethylene.gro...
Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
chain #res #atoms
1 ' ' 1 6
No occupancies in Ethylene.gro
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
Processing chain 1 (6 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581
Fatal error:
Residue 'ETY' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I am kind of baffled what could be wrong. I would really appreciate if you
could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
doubt)?
Do i have to edit esiduetypes.dat?
Thank you many times for your precious time,
On 4 April 2013 17:21, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/4/13 11:38 AM, Juliette N. wrote:
>
>> Dear all,
>>
>> I am having trouble creating topology file for simple molecule ethylene.
>> Here is the steps. Below is the pdb file:
>>
>> Ethylene.pdb:
>>
>>
>> ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00
>> C
>> ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00
>> C
>> ATOM 3 H11 ETY 1 1.238 -0.928 0.000 1.00 0.00
>> H
>> ATOM 4 H12 ETY 1 1.238 0.928 0.000 1.00 0.00
>> H
>> ATOM 5 H21 ETY 1 -1.238 -0.928 0.000 1.00 0.00
>> H
>> ATOM 6 H22 ETY 1 -1.238 0.928 0.000 1.00 0.00
>> H
>> END
>>
>> Then:
>> editconf -f Ethylene.pdb -o Ethylene.gro
>>
>> Ethylene.gro:
>>
>> 6
>> 1ETY C1 1 0.067 -0.000 0.000
>> 1ETY C2 2 -0.067 -0.000 0.000
>> 1ETY H11 3 0.124 -0.093 0.000
>> 1ETY H12 4 0.124 0.093 0.000
>> 1ETY H21 5 -0.124 -0.093 0.000
>> 1ETY H22 6 -0.124 0.093 0.000
>> 0.00000 0.00000 0.00000
>>
>>
>> Then I add the following residue for ethylene to the rtp file
>> ffoplsaa.rtp:
>>
>> [ ETY ]
>> [ atoms ]
>> C1 opls_143 -0.120 1
>> H11 opls_144 0.060 1
>> H12 opls_144 0.060 1
>> C2 opls_143 -0.120 2
>> H21 opls_144 0.060 2
>> H22 opls_144 0.060 2
>>
>> [ bonds ]
>> C1 H11
>> C1 H12
>> C1 C2
>> C2 H21
>> C2 H22
>> C2 C1
>>
>>
> "C1 C2" and "C2 C1" are redundant. You don't need both.
>
>
> and then
>>
>> ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa
>>
>> Q1_ i dont realize what is the difference between the already created
>> Ethylene.gro and the one in the pdb2gmx(GRO.gro). I am not getting the
>> latter and was wondering what would be the diffrence?
>>
>>
> pdb2gmx produces an output coordinate file as a byproduct of its massively
> complicated fix-build-process procedure.
>
> If you're not getting the output file(s), then pdb2gmx is failing and
> should produce obvious error messages.
>
>
> Q2) Below is the top file which is not generated. Once I Issue pdb2gmx, I
>> enter "6" because pdb2gmx output says:
>>
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/watermo$
>> 1: TIP4P TIP 4-point, recommended
>> 2: TIP3P TIP 3-point
>> 3: TIP5P TIP 5-point
>> 4: SPC simple point charge
>> 5: SPC/E extended simple point charge
>> 6: None
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/aminoac$
>> No occupancies in Ethylene.gro
>> Opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/atomtyp$
>>
>> And finally I get a blank top file::
>>
>> ; File 'Ethylene.top' was generated
>> ; By user: onbekend (0)
>> ; On host: onbekend
>> ; At date:
>> ;
>> ; This is a standalone topology file
>> ;
>> ; It was generated using program:
>> ; pdb2gmx - VERSION 4.5.4
>> ;
>> ; Command line was:
>> ; pdb2gmx -f Ethylene.pdb -o GRO.gro -p Ethylene.top -ff oplsaa
>> ;
>> ; Force field was read from the standard Gromacs share directory.
>> ;
>>
>> ; Include forcefield parameters
>> #include "oplsaa.ff/forcefield.itp"
>>
>>
>> -------------------------
>> output says:
>>
>> Select the Water Model:
>> Reading Ethylene.gro...
>> Read 'GROningen Mixture of Alchemy and Childrens' Stories', 6 atoms
>> Analyzing pdb file
>> Splitting PDB chains based on TER records or changing chain id.
>> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
>>
>> chain #res #atoms
>> 1 ' ' 1 6
>>
>> Reading residue database... (oplsaa)
>> Processing chain 1 (6 atoms, 1 residues)
>> Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the
>> behavior.
>>
>>
> There should be more output after this line. Any reason for pdb2gmx to
> fail would be printed here.
>
>
>
>>
>> Is there something wrong with my rtp? Could I trouble you to let me know
>> what wrong is?
>>
>>
> I can see nothing wrong. I was able to produce a sensible topology using
> all of your input files.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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--
Thanks,
J. N.
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