[gmx-users] problem with phosphorylated serine

[Justin Lemkul]

On 11/17/14 1:25 PM, Jayant James wrote:
> Hi!
> I had actually downloaded the *gromos43a1p-4.5.1.tgz (47 KB) file, *it
> was not the ffG43a1p.tar.gz as said earlier. Sorry about the
> miscommunication.
> So *gromos43a1p-4.5.1.tgz *file was unpacked and placed in
>
> /share/apps/gromacs/4.5.4/single/share/gromacs/top/ and it creates the
> gromos43a1p.ff directory. Under the directory are the files
>
> aminoacids.c.tdb  aminoacids.rtp  ffnonbonded.itp
> aminoacids.hdb    atomtypes.atp   forcefield.doc
> aminoacids.n.tdb  ffbonded.itp    forcefield.itp
>

For some reason the tarball is missing several files, notably the .r2b file that 
prevents the error you are seeing.  I uploaded a new tarball with the full file 
set.  Please download it and try again.

-Justin

> I wonder why I am getting the same error as HISE not found. Also the
> pdb2gmx reads the input file and stops reading when it encounters the
> phosphorylated serine's coordinates, notated as SEP. So is it the correct
> spot to unpack the phosphorylated files?
> Thanks
> JJ
>
>
> On Mon, Nov 17, 2014 at 10:29 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/16/14 8:26 PM, Jayant James wrote:
>>
>>> Hi !
>>> I downloaded the ffG43a1p.tar.gz
>>> <http://www.gromacs.org/@api/deki/files/12/=ffG43a1p.tar.gz> for
>>> simulations of phosphorylated serines (downloaded from
>>> http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
>>> running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
>>> error (below). Well there is no "HISE" in the input pdb file. There is a
>>> SEP. So I thought I'd better get help from the GMX community. I also found
>>> that if I were to execute a pdb file without any phosphorylated serine the
>>> pdb2gmx runs all the way to the end and the gives the error message
>>> similar
>>> to one below.
>>>
>>>
>> You downloaded the wrong files.  Note there is a specific version for 4.5
>> and onward:
>>
>> http://www.gromacs.org/@api/deki/files/132/=gromos43a1p-4.5.1.tgz
>>
>> -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

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