Dear Ibrahim,
it seems that leap uses the MTRIX[123] records below the CRYST1 record
from your pdb file. Simply delete the complete pdb header from your
input pdb file leaving only a single pair of chains from one MODEL as
ATOM input, and retry.
I could reproduce your reported behaviour:
I downloaded 2klr.pdb, deleted MODEL 2-9 (from 10 in total) thus keeping
only chains A and B comprising MODEL 1, and saved the pdb file with the
complete header. Then, I started tleap, loaded the ff14SB forcefield and
the modified pdb file, then saved that unit in pdb format.
Visual inspection showed a cyclic structure of three dimers, the pdb
file contains six chains.
Then, I deleted only the MTRIXn records from the input pdb file,
repeated the leap procedure, and obtained an output pdb file with only
two chains, as expected.
Hope that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
> Thank you in advance. My file is 2KLR.pdb. It contains 10 dimers. I remove
> 9 of these dimers and save only single dimer using UCSF Chimera-1.15.
>
> On Wed, Feb 9, 2022 at 11:17 PM David A Case <david.case.rutgers.edu> wrote:
>
>> On Wed, Feb 09, 2022, Ibrahim Said wrote:
>>
>>> I'm using Amber 16. When using xleap to create *.prmtop and *.rst7 for a
>>> protein in dimer form, xleap adds many extra dimers and forms cyclic
>>> structure. Please, can someone help me.
>>
>> If looking at the TER cards doesn't help, we would need to know details,
>> and
>> probably the contents (and origin) of whatever PDB file you are using.
>>
>> ...thx...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 10 2022 - 03:00:02 PST
