Hi,
Actually , residue 823 is the GDP ..AS There are three chains in the
> structure so there are three GDPs in the Pdb file...they are rsidue 823 ,
> 824 and 825... Problem is leap is recognizing one of them only
Do you mean that the GDP is a single residue made up of three GDPs, or
there are three distinct GDPs or as David mentioned, alternate conformers?
I don't think leap would read in the same molecule with different residue
numbers as a duplicate atom.
As for a fix, you can double check to see if the residue numbers in the pdb
file actually are separate in that each GDP molecule is actually named 823,
824, and 825- the error you're getting makes it sound like they're not
distinct and have the same residue numbers.
If that isn't the issue, then you can try renaming your atoms in each GDP
so that they don't repeat. Since C1 appears once per GDP molecule, you'd
name the second one C1x, the third C1y, and so forth to make sure none of
the atoms you have repeat. If you do that, you might have to play around
with some frcmod/lib files so leap can properly read and ID the atoms.
Best,
Kenneth
On Wed, Sep 16, 2015 at 6:27 AM, ankita mehta <mehtaroadies.gmail.com>
wrote:
> Actually , residue 823 is the GDP ..AS There are three chains in the
> structure so there are three GDPs in the Pdb file...they are rsidue 823 ,
> 824 and 825... Problem is leap is recognizing one of them only ...when i
> generate the structure from topology and inpcrd there is only one
> gdp.......so i said structure is faulty.....tell me the way out how should
> i rename them i mean where should i do this.............so that leap
> recognizes all three differently......
> thnks in advance!
>
> On Wed, Sep 16, 2015 at 12:01 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Tue, Sep 15, 2015, ankita mehta wrote:
>>
>> > I am trying to create topology and coordinate file for the pdb
>> attached..
>> >
>> > It gives the warnings while reading the structure and when these
>> warnings
>> > are ignored and toplogy and coordinate file is generated , structure is
>> > faulty ........
>>
>> To expand on the previous answer: read the warnings carefully. If you in
>> fact
>> have alternate conformers for residue 823 in your input pdb file, LEaP
>> may be
>> doing what you want (selecting the first conformer).
>>
>> >
>> > Warning: Atom names in each residue should be unique.
>> > (Same-name atoms are handled by using the first
>> > occurrence and by ignoring the rest.
>> > Frequently duplicate atom names stem from alternate
>> > conformations in the PDB file.)
>> >
>>
>> Since there weren't any other warnings (e.g. about missing heavy atoms),
>> I'm
>> guessing(?) that you have alternate conformers in the input PDB file.
>>
>> If that is correct, you will need to explain what you mean by the
>> statement
>> "structure is faulty".
>>
>> ...dac
>>
>>
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>
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Received on Wed Sep 16 2015 - 06:00:07 PDT
