[gmx-users] Missing Residues of PDB file

[RINU KHATTRI]

hello justin but what is the use of this command -missing for at least
one missing residues shall we use this or not

On Mon, Aug 25, 2014 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/25/14, 1:31 AM, RINU KHATTRI wrote:
>>
>> use -missing in last of command pdb2gmx
>>
>
> This is extremely dangerous and in should not be done in the case of missing
> residues as it will lead to a broken and useless topology.
>
> -Justin
>
>
>> On Mon, Aug 25, 2014 at 10:54 AM, neha bharti <nehabharty123 at gmail.com>
>> wrote:
>>>
>>> Hello All
>>>
>>> I am performing Molecular dynamics simulation of protein-ligand complex
>>> using charmm36 force field in popc lipid.
>>>
>>> I downloaded the protein ligand complex pdb file. And as mentioned in
>>> Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand
>>> and
>>> protein from pdb file.
>>>
>>> My protein contain some missing residues so I have homology modeled the
>>> protein taking the same pdb file as target and templet.
>>>
>>> At the time of Building the complex step I am using the homology modelled
>>> protein.
>>>
>>> Can I add the ligand in that file as shown in tutorial:
>>>
>>>    163ASN      C 1691   0.621  -0.740  -0.126
>>>    163ASN     O1 1692   0.624  -0.616  -0.140
>>>    163ASN     O2 1693   0.683  -0.703  -0.011
>>>      1JZ4  C4       1   2.429  -2.412  -0.007
>>>      1JZ4  C14      2   2.392  -2.470  -0.139
>>>      1JZ4  C13      3   2.246  -2.441  -0.181
>>>      1JZ4  C12      4   2.229  -2.519  -0.308
>>>      1JZ4  C11      5   2.169  -2.646  -0.295
>>>
>>> because due to homology modeling it might be possible that the
>>> coordinates
>>> of the protein will get change??
>>>
>>> Or I should use maxwarn option to avoid the error message of missing
>>> residues of protein pdb file and no need of homology modelling??
>>>
>>> Please Help
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>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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