Thanks very much for your advice. I just adjusted the script to include
only the chain with mutation,
#!/bin/sh
#
#
parmed="python $AMBERHOME/bin/parmed.py"
$parmed protein_vdw_bonded.parm7 <<_EOF
loadRestrt protein_vdw_bonded.rst7
setOverwrite True
tiMerge :1-99 :199-297 :32 :230
outparm merged_protein_vdw_bonded.parm7 merged_protein_vdw_bonded.rst7
quit
_EOF
But this merging procedure failed, and the error message is like the
following:
> Merging molecules [:1-99] [:199-297] with sc mask [:32] [:230]
Action tiMerge failed
instance: mol1mask and mol2mask must be adjacent in topology.
Recreate topology with the molecules to be merged adjacent in the
PDB file.
So, is there anything wrong with my script ?
> Have you tried to include only the chain with the mutation in the mask ?
> This would also require you to write the second chain only once into the
> parmtop file.
> In practice, there is really no need to duplicate more molecules than
> necessary.
> ________________________________________
> From: jfliu.itcs.ecnu.edu.cn [jfliu.itcs.ecnu.edu.cn]
> Sent: 03 April 2016 14:29
> To: amber.ambermd.org
> Subject: [AMBER] How to use tiMerge properly in pmemd TI calculation
>
> Dear Amber users,
>
> I want to calculate the ralative binding free energy for a ligand to
> the mutated protein through the TI calculation. However, I got
> something wrong when I tried to get the merged prmtop file. The
> protein has two chains, in which the residue sequence are 1-99 and
> 100-198, respectively. The mutation is on residue 32. To get the
> merged prmtop file, I used the following script:
>
> #!/bin/sh
> #
> #
>
> parmed="python $AMBERHOME/bin/parmed.py"
>
>
> $parmed protein_vdw_bonded.parm7 <<_EOF
> loadRestrt protein_vdw_bonded.rst7
> setOverwrite True
> tiMerge :1-198 :199-396 :32 :230
> outparm merged_protein_vdw_bonded.parm7 merged_protein_vdw_bonded.rst7
> quit
> _EOF
>
> And some of the output was:
>
>> Merging molecules [:1-198] [:199-396] with sc mask [:32] [:230]
> MoleculeWarning: Molecule atoms are not contiguous! I am attempting to fix
> this,
> Merging molecules :1-198 and :199-396 into the same molecule.
> Use softcore mask:
> timask1='.497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512',
> timask2='.3136,3137,3138,3139,3140,3141,3142,3143,3144,3145,3146,3147,3148,3149,
> scmask1='.497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512',
> scmask2='.3136,3137,3138,3139,3140,3141,3142,3143,3144,3145,3146,3147,3148,3149,
>
> In the above output, I found the timask2 and scmask2 are wrong atoms. And
> I checked the merged pdb file, I found the mutated residue was attached at
> the end of the first chain of protein, and the correct atom number should
> be 1568-1586. So in the following TI run, I got the error message "Error :
> Atom 497 does not have match in V1 !".
>
> Can anyone tell me where the problem is ? By the way, if the protein has
> only one chain, I can definitely get the right timask2 and scmask2.
>
> Thanks in advance !
>
> Jinfeng
>
>
> _______________________________________________
> 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 Sun Apr 03 2016 - 07:00:07 PDT
