[gmx-users] pdb2gmx and atomtype.atp
Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 3 17:22:04 CET 2010
Please file a bugzilla, uploading all of the input files needed to reproduce the
problem. It appears that you can cause LP2 to be assigned an LP type if it is
the first line in atomtypes.atp, but the mass and charge are still nonsense.
Certainly you can manually modify the topology to fix this problem, but it is
definitely an important bug worth fixing.
-Justin
Sarath Chandra wrote:
> Gromacs version used was 4.5.3. I have added the new atomtype LP in the
> atomtype.atp and I have also defined the nonbonded+bonded interactions
> for LP. Parameters for LP were obtained from /Dixon.et.al
> <http://Dixon.et.al> J.Comp.Chem, 18, 1632-1646/
>
>
> *atomtypes.atp entry---------------*
>
> LP 3.00000 ;
>
>
> *ffnonbonded.itp entry------*
>
> LP 0 3.000 0.0000 A 0.00000e+00 0.00000e+00 ;
>
>
> *rna.rtp entry.........*
>
> [ ATEM ]
> [ atoms ]
> CL CT 0.18734 1
> HCL HC 0.08035 2
> CT1 CT -0.07300 3
> HT11 HC 0.02400 4
> HT12 HC 0.02400 5
> CT2 CT -0.07300 6
> HT21 HC 0.02400 7
> HT22 HC 0.02400 8
> CT3 CT 0.18900 9
> C31 CT -0.08900 10
> H311 HC 0.02700 11
> H312 HC 0.02700 12
> H313 HC 0.02700 13
> C32 CT -0.08900 14
> H321 HN 0.02700 15
> H322 HN 0.02700 16
> H323 HN 0.02700 17
> CT4 CT 0.18900 18
> C41 CT -0.08900 19
> H411 HN 0.02700 20
> H412 HN 0.02700 21
> H413 HN 0.02700 22
> C42 CT -0.08900 23
> H421 HC 0.02700 24
> H422 HC 0.02700 25
> H423 HC 0.02700 26
> NT5 NN 0.03700 27
> OT5 ON -0.11800 28
> LP1 LP -0.11000 29
> LP2 LP -0.11000 30
>
>
>
>
> On Fri, Dec 3, 2010 at 4:40 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sarath Chandra wrote:
>
> Dear Gromacs users,
>
>
> I have a nitroxide radical with lone pairs on oxygen which has
> to be attached to Adenine of a RNA. I have the forcefiled for
> the nitroxide radical and as well as i have obtained the charges
> for the link atoms using resp. I use specbond.dat to make the
> link between the nucleotide and the radical molecule and all of
> that goes well. The problem comes in the topol.top file.
> Lonepair on oxygen has an atom type LP and I have two lone pairs
> LP1 and LP2.
>
> The atomtype charge and mass for LP1 are assigned properly but
> for the LP2 atomtype is that of 'Br' and charge is 0 mass is
> just weird.
>
> topol.top output__________________________________________
>
> 445 ON 14 ATEM OT5 445 -0.118
> 16 ; qtot -11.78
> 446 LP 14 ATEM LP1 446 -0.11
> 3 ; qtot -11.89
> 447 Br 14 ATEM LP2 447 0
> 1.48594e-41 ; qtot -11.89
>
>
> If i interchange the first two lines of the atomtypes.atp, for
> LP2 i get atomtype 'C'
>
> C 12.01000 ; sp2 C carbonyl group
> Br 79.90000 ; bromine
>
>
> This indicates to me that pdb2gmx is failing to find an appropriate
> atom type and is instead simply assigning the first type it comes
> to, yielding undefined charges and masses.
>
>
> If there was a problem with the forcefield files the error in
> assigning atomtypes should happen for both LP1 and LP2. I have
> played with the atom names using LPx and LPy, the error repeats
> with LPy and I also changed the atom lines order in the pdb
> file. I can simply correct the atomtype, mass, charge and my
> simulation works well. No problems with grompp either. I have
> checked the line spacings and they are all fine. I was just
> wondering if there is something I have overlooked or if it was a
> bug.
>
>
> There isn't an "LP" type by default in atomtypes.atp for
> amber99sb.ff; have you added it? What's in your .rtp file? You
> haven't shown us any relevant input, so it's impossible to diagnose
> whether this is a Gromacs problem or just something you've overlooked.
>
> -Justin
>
>
> ____________________
>
> A small second issue to report that if you introduce a blank
> line (either for fun or by mistake) at the end of the
> atomtypes.atp file, pdb2gmx hangs and stays like that until you
> kill it
>
> pdb2gmx output................
> _____________
>
> Opening force field file
> /home/dsarath/Utilities/share/451//amber99sb.ff/aminoacids.r2b
> Opening force field file
> /home/dsarath/Utilities/share/451//amber99sb.ff/dna.r2b
> Opening force field file
> /home/dsarath/Utilities/share/451//amber99sb.ff/rna.r2b
> Reading Test-5T.pdb...
> Read 'Great Red Owns Many ACres of Sand', 447 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 14 residues with
> 447 atoms
>
> chain #res #atoms
> 1 ' ' 14 447 All occupancies are one
> Opening force field file
> /home/dsarath/Utilities/share/451//amber99sb.ff/atomtypes.atp
> Atomtype 1
>
> -------------------here pdb2gmx hangs
>
>
>
> Best Wishes,
>
>
> Sarath
>
> ________________
>
> Sarath Chandra Dantu
> Computational Biomolecular Chemistry
> Max Planck Institute of Biophysical Chemistry
> Am Fassberg 11,
> Gottingen
> 37077
> Germany
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list