[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Even when I add the new atom types to aminoacid.rtp, .hdb ,   .atp ,
Still it shows the same error ....

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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