[gmx-users] problem with phosphorylated serine

[Jayant James]

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

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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-- 
Jayasundar Jayant James

http://www.chick.com/reading/tracts/0076/0076_01.asp