Ok, I got it. Thank you very much !
> 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 - 07:30:04 PDT
