[gmx-users] problem with phosphorylated serine

[Jayant James]

Hi!
Thanks it did work after I added "SEP    Protein" to the residuetypes.dat
file. While executing pdb2gmx I found that I am asked to choose the water
model and I choose SPC. Then I got the error that stating that (Error
message below).

Error Message
-------------
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2gmx.c, line: 1879
Fatal error:
The topology file 'gromos43a1p.ff/spc.itp' for the selected water model
'spc' can not be found in the force field directory. Select a different
water model.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


Hence I went and listed the files in the non-phosphorylate and
phosphorylated directories and found that many files in the
non-phosphorylated directory are *not *present in the phosphorylated
directory (given below)

$ ls gromos43a1.ff/
aminoacids.c.tdb  *aminoacids.vsd  * forcefield.doc   *spce.itp*
aminoacids.hdb    atomtypes.atp    forcefield.itp   *spc.itp*
aminoacids.n.tdb  ffbonded.itp     *ions.itp         tip3p.itp*
aminoacids.r2b    *ff_dum.itp       methanol216.gro*  *tip4p.itp*
aminoacids.rtp    ffnonbonded.itp  *methanol216.gro*  watermodels.dat

$ ls gromos43a1p.ff/
aminoacids.c.tdb  aminoacids.rtp   forcefield.doc  watermodels.dat
aminoacids.hdb    atomtypes.atp    forcefield.itp
aminoacids.n.tdb  ffbonded.itp     MD5SUM.txt
aminoacids.r2b    ffnonbonded.itp  README

SO MY QUESTION IS: Is it ok to copy these files that are missing in the
phosphorylated force field directory from the non-phosphorylated
force field directory?

Thank you
JJ


On Mon, Nov 17, 2014 at 11:40 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
>>> ==================================================
>>> --
>>> 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 629
> 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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-- 
Jayasundar Jayant James

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