[AMBER] How to use tiMerge properly in pmemd TI calculation

From: <jfliu.itcs.ecnu.edu.cn>
Date: Sun, 3 Apr 2016 13:29:11 -0000

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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Received on Sun Apr 03 2016 - 07:00:04 PDT
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