sir,
sorry I have missed one line. There would be one extra line. After
loading library file ..
> hca = loadpdb 2CBA.pdb
sanjib
On 7/16/12, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Jul 16 2012 - 04:00:04 PDT
