[gmx-users] Missing Residues of PDB file

[Justin Lemkul]

On 8/27/14, 6:25 AM, RINU KHATTRI wrote:
> hello justin but what is the use of this command -missing for at least
> one missing residues shall we use this or not
>

For a missing residue within the chain, you should absolutely not use -missing. 
  If you do, you will have a flawed model that will almost certainly crash, and 
if it manages to run it's still not physically reasonable.

The only legitimate use of -missing would be in niche cases where you might be 
trying to build model compounds or fragments based off of existing residues for 
whatever purpose, e.g. if I want to do a simulation of united-atom phenol, I 
could use -missing when processing a coordinate file containing a residue name 
TYR but without the backbone atoms.

-Justin

> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
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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
http://mackerell.umaryland.edu/~jalemkul

==================================================