VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Oct 05 2017 - 01:21:10 CDT

If you are using CGenFF output, I strongly suggest that you use the tool in the BuildBar-> Prepare Parameriation from CGenFF Program Output tab to generate the required PSF/PDB and the resulting parameters as initial inputs. When combined with the standard par_all36_cgenff.prm this should comprise all necessary parameters to perform the optimization/refinements.

Regards,
Christopher Mayne

> On Oct 4, 2017, at 1:01 PM, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>
> I can find no such improper term in the cgenff par file. Maybe it’s including in the str file generated by paramchem? Can you copy and paste the text of the str file you got, if it’s not too much? Alternatively, send just this file to me off-list. In general, you should always hit reply-all when emailing people through the mailing list.
>
> Best,
> JC
>
>> On Oct 3, 2017, at 9:02 PM, RAHUL SURESH <drrahulsuresh_at_gmail.com <mailto:drrahulsuresh_at_gmail.com>> wrote:
>>
>> Dear JC
>>
>> On Wed, 4 Oct 2017 at 3:51 AM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>> OG2D1 is (typically) an atom type, so it’s fine to be repeated. I doubt it’s the name, which would be in the first column (type in the second) of the topology (str) file.
>>
>> FFTK doesn’t treat impropers (we’ve found their actually relatively easy/better to do by hand anyway). So any improper must be coming from paramchem. Are you also loading the cgenff parameter file? “str” stands for “stream”, meaning that you still usually need a parent cgenff parameter file to go with it. Maybe the improper is in there?
>>
>>
>> Yes. I am using the parachem file. I get the stream file from chenn server and use that to parameterize the molecule using ffTK. Without the improper dihedrals it shows that the dihedrals are missing and after adding it manually now it shows that the improper dihedrals are misrepresented.
>>
>> What can be done with this.?
>>
>> Thank you
>>
>> Best,
>> JC
>>
>>> On Oct 3, 2017, at 6:44 AM, RAHUL SURESH <drrahulsuresh_at_gmail.com <mailto:drrahulsuresh_at_gmail.com>> wrote:
>>>
>>> During my dihedral optimisation,
>>>
>>> The error call is as follows
>>>
>>> FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
>>> LINE=*CG2O1 CG301 NG2S1 OG2D1 0.0000 ! *
>>>
>>> Earlier i had an error stating
>>>
>>> Charm++ fatal error:
>>> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O1 CG301 NG2S1 OG2D1 (ATOMS 12 7 14 13)
>>>
>>> So I manually added the improper angle to the parameter file.
>>>
>>> I note that two oxygen atom in the molecule are having same name OG2D1. The naming was done from the str file generated using cgenff.parachem server.
>>>
>>> Thanks in advance
>>>
>>> --
>>> Regards,
>>> Rahul Suresh
>>> Research Scholar
>>> Bharathiar University
>>> Coimbatore
>>
>> --
>> Regards,
>> Rahul Suresh
>> Research Scholar
>> Bharathiar University
>> Coimbatore


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