[gmx-users] Creating Custom .rtp files

[Justin Lemkul]

On 8/2/17 5:07 AM, Momin Ahmad wrote:
> I think the reason for the weird log is the "|&tee" command that lets you write 
> the output of another command into a file. In the case of the error i could 
> choose the forcefield before the error occurred. The methane was called "CH4" 
> before, i just changed the names for troubleshooting. This time i did copy&paste 
> manually. Files are attached. There are two comments that show the differences 
> in the versions. Again: the two .rtp files for both versions are identical and 
> the same .pdb file is used.
> 

Works fine for me using the files you provided on Redmine.  I suspect you're 
just not managing your files correctly.  Make sure your methane.rtp is in the 
force field subdirectory, not the working directory or anywhere else.

-Justin

> 
> Am 01.08.2017 um 20:42 schrieb Justin Lemkul:
>>
>>
>> On 8/1/17 10:32 AM, Momin Ahmad wrote:
>>> please finde the files attached to this email: log-files for the 5.1.2 
>>> version and the 2016.3 version, also again the .rtp file and the .pdb file
>>>
>>
>> The screen output seems garbled to me, with the fatal error coming before the 
>> force field selection, and multiple locations being used. I can't figure out 
>> what's going on.  Your .rtp needs to be in the force field directory that you 
>> choose, either locally (within the working directory) or system-wide (wherever 
>> that is installed).  Note also that "CH4" and "CH41" are different, because 
>> one error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41.
>>
>> -Justin
>>
>>>
>>> Am 01.08.2017 um 00:48 schrieb Justin Lemkul:
>>>>
>>>>
>>>> On 7/31/17 7:47 AM, Momin Ahmad wrote:
>>>>> Hello,
>>>>>
>>>>> the .rtp file is located in the same directory as the force-field. When i 
>>>>> type gmx gmx2pdb ..... then the log shows that the right path is considered 
>>>>> and loads the needed .rtp fiels that already exist in the forc-field file. 
>>>>> But my custom one is ignored.
>>>>>
>>>>
>>>> Please post the full screen output of pdb2gmx, including the force field 
>>>> selection.  If your .rtp file is not being read, it is likely misformatted, 
>>>> in which case you should either write your new residue entries in an 
>>>> existing file or upload it to a file-sharing service so we can provide 
>>>> feedback.
>>>>
>>>> -Justin
>>>>
>>>>> Greets
>>>>> Momin Ahmad
>>>>>
>>>>> Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:
>>>>>> On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad <momin.ahmad at kit.edu> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I created a custom .pdb file and the associated .rtp file for the
>>>>>>> force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the
>>>>>>> 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
>>>>>>> version is a local installation in my /home/user folder. The log shows
>>>>>>> the correct paths but does not consider my custom .rtp file.
>>>>>> I would recommend to check whether the rtp file location and source where
>>>>>> gmx  you have installed match. Apart from that I do not think any error
>>>>>> with version of Gromacs.
>>>>>>
>>>>>>> Am i doing
>>>>>>> something wrong with the newer version? I added two simple files of my
>>>>>>> problem. Thanks in advance.
>>>>>>>
>>>>>>> Cheers
>>>>>>> Momin Ahmad
>>>>>>> Karlsruher Institut of Technology
>>>>>>> Germany
>>>>>>> -- 
>>>>>>> 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

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