Hi Filipa,
Another thing I want to say is that for Mg2+ ions, a nonbonded model can usually do a reasonable work because of the ionic character of Mg2+. In this way you do not need to do a MCPB.py modeling for your system, while a normal 12-6 nonbonded model (
https://ambermd.org/tutorials/advanced/tutorial20/12_6.htm <
https://ambermd.org/tutorials/advanced/tutorial20/12_6.htm>) could be a reasonable choice.
Pengfei
> On Mar 27, 2020, at 5:21 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Filipa,
>
> I think there may be inconsistency between your mol2 file(s) and the PDB file. Or you do not have the metal ion(s) meet the following requirement that is stated in the tutorial (http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>):
>
> MCPB.py now supports more than 80 metal ions (see Figure 3 in the reference paper <http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>). For all of these metal ions and halide ions (if in the ion format but not neutral format), capitalized element name are suggested to use for both the residue name and atom name. Please make sure the residue name and atom name of the metal ion (not only for zinc used here) are all captilized (e.g. herein all equals "ZN", not "Zn", "zN", or "zn"), only in this way MCPB.py will recognize it as a metal ion. Meanwhile, please make sure each metal ion or halide ion (if it is in its ion format but not neutral format) is treated seperately as an indepedent residue in the PDB file. If you have metal site which has metal ion embeded in the ligand residue, for example, the HEME group in PDB file, please seperate the metal ion into an independent residue (also, with an unique residue number and atom number)in the PDB file. Meanwhile, in order to make MCPB.py recognize the atoms well, if you have atoms have atom names capitalized with numbers in your original PDB file (applies for protein or ligand), please change these atom names to atom names capitalized with their element symbols (for example, change "2HA1" to "HA12", change "1HAA" to "HAA1") in the PDB file before performing following steps.
>
> Hope it helps,
> Pengfei
>
>> On Mar 4, 2020, at 12:00 PM, Filipa Mendonça <filipa_de_mendonca.hotmail.com <mailto:filipa_de_mendonca.hotmail.com>> wrote:
>>
>> Dear All,
>>
>> I'm trying to refine the active center of my protein.
>> The active center has two MG ions, so I've tired to use the tutorial of MCPB.py.
>> However, when I try to run my model.in file, I have the folloying error:
>> What can I do to solve this problem?
>>
>> *=======================Metal Site Information===================*
>>
>> * *
>>
>> ******************************************************************
>>
>> ***Selected Metal ion MG is atom 20248 in residue 1259-MG
>>
>> ***Selected Metal ion MG is atom 20249 in residue 1260-MG
>>
>> 729-ASP.OD1 is in 2.8 Angstrom of or set bonded (in the input file) to (one of) these metal ions
>>
>> ***The following residues are in the Metal Site:
>>
>> Residue 729-ASP
>>
>> Residue 1259-MG
>>
>> Traceback (most recent call last):
>>
>> File "/miniconda2/miniconda3/bin/MCPB.py", line 644, in <module>
>>
>> addred, lgchg, lgspin)
>>
>> File "/miniconda2/miniconda3/lib/python3.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 1692, in gene_model_files
>>
>> totchg = totchg + chargedict[mol.residues[i].resname]
>>
>> KeyError: 'MG'
>>
>>
>> Best Regards,
>> Filipa Mendonça
>>
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>
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Received on Fri Mar 27 2020 - 14:30:02 PDT
