I think the error message means that you need to write the first chain into the topology file such that the second copy immediatly follows the first one. Then you append all those components that you will not alter with parmed. You will have to adjust the mask such that they correspond to the new arrangment.
________________________________________
From: jfliu.itcs.ecnu.edu.cn [jfliu.itcs.ecnu.edu.cn]
Sent: 03 April 2016 14:55
To: AMBER Mailing List
Subject: Re: [AMBER] How to use tiMerge properly in pmemd TI calculation
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
>
>
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>
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>
>
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Received on Sun Apr 03 2016 - 07:30:03 PDT
