[gmx-users] (no subject)

[Justin Lemkul]

On 11/8/16 6:13 AM, Kingsley Theras Primus Dass . wrote:
> Even when I add the new atom types to aminoacid.rtp, .hdb ,   .atp ,
> Still it shows the same error ....
>

The error has nothing to do with atom types, and without seeing what you did, 
there's no possible way to solve it.  An anionic sulfotyrosine residue should 
have the same .hdb entry as normal tyrosine.  Copy it and rename the residue to 
whatever your .rtp specifies.

-Justin

> Could you please suggest some solutions.
>
> Thank you in advance
>
> On 8 Nov 2016 6:59 p.m., "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
>>
>>> Hello users!!
>>>
>>> I generated a Topology file for SO3- using ATB topology generator , which
>>> is compatible with GROMACS. Then I copied the .rtp file from ATB and
>>> pasted
>>> it into  GROMACS aminoacid.rtp.
>>>
>>>  The  partial charge of aminoacid sulfated-tyrosine was -1.
>>> When I run -pdb2gmx there was error saying the atoms were missing ,
>>> -------------------------------------------------------
>>> Program gmx pdb2gmx, VERSION 5.1
>>> Source code file:
>>> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce
>>> ss/pdb2top.cpp,
>>> line: 1584
>>>
>>> Fatal error:
>>> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
>>> this incomplete topology anyhow, use the option -missing
>>>
>>>
>>> then I ran pdb2gmx -ignh -p topol.top -missing
>>>
>>> It generated the topology file. But the parital charge of sulfated
>>> tyrosine
>>> was changed to -2, coz of missing hydrogen atoms.
>>>
>>> can you please suggest some solutions , to overcome this problem.
>>>
>>>
>> Add an .hdb entry for your residue so that pdb2gmx will build the missing
>> atoms.  In general, never use the -missing option.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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