Sorry, please ignore my last email:
"note: they both have +1 charge."
Inadvertently pressed reply to the wrong message.
Best,
Brandon
On Wed, Jun 27, 2012 at 3:10 PM, Brandon Sim <simpavid.gmail.com> wrote:
> note: they both have +1 charge.
>
>
> On Wed, Jun 27, 2012 at 3:09 PM, Brandon Sim <simpavid.gmail.com> wrote:
>
>> Dear all,
>>
>> A PDB file I am working on has several missing residues, so I added them
>> in manually by copying and pasting the residue info in from another similar
>> PDB file that does have those residues. However, as expected, the bond
>> lengths between these residues is a bit off (~4 angstroms).
>>
>> I was hoping that sander would just snap these bonds back into place
>> during minimization and would fix the problem. However, when I am preparing
>> the inpcrd and parmtop files through tleap, it keeps thinking that because
>> of the long distance between the atoms mentioned before, the two belong to
>> separate molecules; hence, tleap adds in HXT to the end of the preceding
>> residue.
>>
>> Is there a way I can stop tleap from doing this?
>>
>> Thanks,
>> Brandon
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 27 2012 - 12:30:03 PDT
