[gmx-users] termini modification

[Justin A. Lemkul]

lina wrote:
> pdb2gmx -ter
> 

I doubt this is of any use; the Amber force fields don't use the same 
conventional termini selection that the other force fields do, as the OP states. 
  I suspect that's why the .tdb approach is not working.

I think the best approach is to simply write .rtp entries for the modified 
terminal residues with unique names such that they are distinguished from all 
other residues.  I don't know if it will work (since termini in Amber are 
treated differently), but it's worth a try.

-Justin

> On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj <vijayaraj81 at gmail.com> wrote:
>> Hello,
>>
>> I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
>> terminal residues from NALA and CALA to normal ALA (just as middle
>> residues). As the terminal selection option is not enabled with the amber
>> ff, I am using the termini modification parameters with aminoacids.c.tdb.
>> here is my code for the aminoacids.c.tdb
>>
>> [ COO- ]
>>
>> [ replace ]
>> H    H    1.00800        0.27190
>> N    N    14.01000    -0.41570
>> CA    CT    12.01000    0.03370
>> HA    H1    1.00800        0.08230
>> C    C    12.01000    0.59730
>> CB    CT    12.01        -0.1825
>> HB1    HC    1.008        0.0603
>> HB2    HC    1.008        0.0603
>> HB3    HC    1.008        0.0603
>>
>> [ add ]
>> 1    1    O    C    CA    N
>>         O    16.00000    -0.56790
>>
>> [ bonds ]
>> C    O     1    0.12290        476976.0
>>
>> [ delete ]
>> OC1
>> OC2
>>
>>
>> when I run pdb2gmx using this termini modification, everything works fine
>> except the deletion of OC1 and OC2 atoms, the error which I get for this run
>> as follows,
>>
>> Fatal error:
>> Atom OC2 not found in residue seq.nr. 8 while adding atom
>>
>>
>> any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
>> delete ] option with the aminoacids.c.tdb file, it works fine by adding the
>> O atom to the terminal residue including the presence of OC1 and OC2 atoms.
>> first I am trying to modify the c terminal residue.
>>
>> Regards,
>> vijay.
>>
>> --
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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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