I had a similar issue with 2 ligands in my protein. I solved it by
separating them into separate files files. I then processed them
separately.
e.g.
antechamber -i ligand_c.pdb -fi pdb -o ligand_c.mol2 -fo mol2 -nc -1 -c bcc
-s 2
antechamber -i ligand_d.pdb -fi pdb -o ligand_d.mol2 -fo mol2 -nc -1 -c bcc
-s 2
parmchk -i ligand_c.mol2 -f mol2 -o ligand_c.frcmod
parmchk -i ligand_d.mol2 -f mol2 -o ligand_d.frcmod
tleap;
loadamberparams ligand_c.frcmod
loadamberparams ligand_d.frcmod
ligc = loadmol2 ligand_c.mol2
ligd = loadmol2 ligand_d.mol2
ligand = combine { ligc ligd }
protein = loadpdb protein_h.pdb
complex = combine { protein ligand }
Nic out
On 09/16/2015 06:27 AM, ankita mehta 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 [1]<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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References
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Received on Wed Sep 16 2015 - 09:00:02 PDT
