tleap fails to include an improper torsion term for the new methyl group in
the DMC residue, i.e.
C7 C4
\ /
C5
|
C6
C6,C4,C5,C7
when writing out the prmtop file. Can anyone help me figure out how best
to add this term? Thank you in advance.
Sid
On Wed, Mar 12, 2014 at 5:01 PM, Sidney Elmer <paulymer.gmail.com> wrote:
> Thank you for the suggestion, David.
>
> There were two gotchas that other's might hit, just like I did:
>
> 1. don't forget to delete the H5 atom in your pdb file
> 2. in order to make the parameters compatible with the amber99SBildn
> force field, I had to change the atom type for the C5' atom to CT
>
>
>
>
> On Wed, Mar 12, 2014 at 12:33 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Mar 12, 2014, Sidney Elmer wrote:
>>
>> > This information was very helpful. I would like to build double
>> > stranded DNA with methylated cytosines directly in NAB using bdna().
>> > I looked through the NAB code and quickly got lost. I'm happy to do
>> > this myself, but I would appreciate some guidance as to how to do
>> > this. Could someone please outline the steps necessary to accomplish
>> > this? Thank you!
>>
>> First, use NAB to build a standard BNDA helix [use fd_helix(), not
>> bdna()].
>> See tutorial B1 for a detailed walk-through on how to do this.
>> An easier alternative for most cases is to visit w3dna.rutgers.edu.
>>
>> Second, edit the PDB file to change the DC residue names to whatever your
>> library is calling methylated cytosine; let LEaP build the structure from
>> the un-methylated structure.
>>
>> ...good luck...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 28 2014 - 12:30:02 PDT
