[gmx-users] Topology file-residue unknown

[Juliette N.]

Thank you Justin. I have now the topology. I have a quick question
regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
these are not the proper atomtypes for H2C=CH2.

rtp entry:

[ 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

>From atomtypes.atp

opls_141   12.01100  ; alkene C (R2-C=)
 opls_142   12.01100  ; alkene C (RH-C=)
* opls_143   12.01100  ; alkene C (H2-C=)
 opls_144    1.00800  ; alkene H (H-C=)*

Did I select the correct atomtypes?
Thanks many times!




On 4 April 2013 18:23, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/4/13 6:17 PM, Juliette N. wrote:
>
>> 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<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?
>>
>>
> You've added the .rtp entry incorrectly.  pdb2gmx in version 4.5 and above
> needs .rtp files to be organized in force field subdirectories (in your
> case oplsaa.ff).  It will not recognize a file called "ffoplsaa.rtp," which
> is the pre-4.5 syntax for force field 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.