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