Respected sir,
What I have done in xleap is like following
>clearpdbresmap
clearing name map
>loadoff zin.off (library file of zinc)
Loading library: ./zin.off
Loading pdb file : ./2CBA.pdb
total atoms in file: 2294
Leap added 2451 missing atoms according to residue templates:
2451 H / lone pairs
The file contained 1 atoms not in residue templates
> set hca head hca.3.1
> pro = sequence { NMET SER hca }
> savepdb pro 2cba_mod.pdb
Here, coordinate of protein changed. But that of water and OXT remain
same. Therefore,position with respect to protein has changed. I want
crystal waters at their previous position. So, sir, what shoul I do?
On 7/15/12, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Jul 15, 2012, Sanjib Paul wrote:
>
>> I am going to set a
>> HCA
>> II protein in AMBER 9. I am using 2CBA pdb which lacks of two starting
>> residues at n-terminal. So, I wanted to add these two residues by x-leap.
>> I
>> have added residues successfully.
>
> You have told us what you intended to do (add the residues [successfully]).
> But you have not told us what you actually *did*. In such a case, people
> on the list can't be of much help.
>
> Adding missing residues in protein crystal structures is not something LEaP
> can do well, expect in very simple circumstances. You might want to
> consider
> using a homology moldeling program.
>
> ....dac
>
>
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Received on Mon Jul 16 2012 - 04:00:03 PDT
