[gmx-users] termini modification
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 27 16:13:26 CEST 2011
> 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.
> On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj <vijayaraj81 at gmail.com> wrote:
>> 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 ]
>> 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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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