(You can be sure you are loading the right file by messing it up to see
if load fails.)
On 12/26/17 4:12 PM, mish wrote:
> Thanks a lot. I did try without the comma, without quotes etc.. but tleap
> doesn't seem to pickup these numbers from frcmod file. Anyways, I will look
> into it carefully if spacing or having number 000 is not the reason.
>
> Best,
> Sushil
>
>
> On Tue, Dec 26, 2017 at 11:12 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
>> Look at the Glycam force field files--those SCEE and SCNB values are not
>> the defaults. It looks like the only difference with your frcmod may be
>> that there is a comma between SCEE=1.0 and SCNB=1.0 (the Glycam frcmod has
>> just blank space). See if you can engage the custom 1:4 scaling factors
>> with a sugar component in your system, to make sure that it's about the
>> frcmod and not something else you are doing or failing to do.
>>
>> Dave
>>
>>
>> On Tue, Dec 26, 2017 at 3:09 AM, mish <smncbr.gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> I wonder if it should be possible to read SCNB and SCEE entries from
>>> frcmod file? I am using AmberTools16. Ligand is a modified GLYCAN and it
>>> has dummy atom. I want to keep SCNB and SCEE to 1.0. The frcmod loaded to
>>> tleap is in the following format:
>>>
>>> -----ligand.frcmod--------
>>> remark goes here
>>> MASS
>>> zz 0.000 0.000 ATTN, need revision
>>> du 0.000 0.000 ATTN, need revision
>>>
>>> BOND
>>> Cg-zz 0.00 0.000 ATTN, need revision
>>> zz-du 0.00 0.000 ATTN, need revision
>>>
>>> ANGLE
>>> C -Cg-zz 0.000 0.000 ATTN, need revision
>>> Cg-zz-du 0.000 0.000 ATTN, need revision
>>> Hc-Cg-zz 0.000 0.000 ATTN, need revision
>>>
>>> DIHE
>>> Ng-C -Cg-zz 1 0.000 0.000 0.000 SCEE=1.0,
>>> SCNB=1.0 ATTN, need revision
>>> C -Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
>>> SCNB=1.0 ATTN, need revision
>>> Hc-Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
>>> SCNB=1.0 ATTN, need revision
>>> zz-Cg-C -O 1 0.000 0.000 0.000 SCEE=1.0,
>>> SCNB=1.0 ATTN, need revision
>>>
>>> IMPROPER
>>>
>>> NONBON
>>> zz 0.0000 0.0000 ATTN, need revision
>>> du 0.0000 0.0000 ATTN, need revision
>>> ----------
>>>
>>> --leap.in--
>>> source leaprc.GLYCAM_06j-1
>>> loadAmberParams "./ligand.frcmod"
>>> s = loadmol2 "./liagnd.mol2"
>>> saveAmberParm s "ligand.parm7" "ligand.rst7"
>>> quit
>>> ---
>>>
>>> I wonder if it is possible to have scnb=scee=1 set to those dihedrals
>>> defined in frcmod file. Currently, leap set it those to default (last two
>>> entries in my case are 1.2 and 2.0):
>>>
>>> --parm7---
>>>
>>> %FORMAT(5E16.8)
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.20000000E+00 1.20000000E+00 0.00000000E+00
>>> 0.00000000E+00
>>> %FLAG SCNB_SCALE_FACTOR
>>> %FORMAT(5E16.8)
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
>>> 1.00000000E+00
>>> 1.00000000E+00 2.00000000E+00 2.00000000E+00 0.00000000E+00
>>> 0.00000000E+00
>>> %FLAG SOLTY
>>> ----
>>>
>>> Sincerely,
>>> Mish
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Tue Dec 26 2017 - 16:30:03 PST
