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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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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
========================================
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