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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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