Jesmita Dhar,
See
http://upjv.q4md-forcefieldtools.org/REDServer-Development/faq.php#5
When describing the problem you encountered with R.E.D. Server
Development, please also provide the 'PXXXX' R.E.D. Server Development
job name in the body of your email so that we can more easily assist
you.
I look at your last job I could find using your email address:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFmyR4WopAADFKhpZR2zZdRFJrMFJ2zyAWADF/P1314.html
& at your input structure using the java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFmyR4WopAADFKhpZR2zZdRFJrMFJ2zyAWADF/P1314/javaapplet-pdbinp-1.html
Your functionalized graphene is correctly handled by PyRED, but I
wonder if some hydrogen atoms are not missing in your input molecule
for instance C #28 does not bear any hydrogen atom???? idem for C #49
??? others ??? to be carefully checked...
Thus because some hydrogen atoms are missing; that means that the
optimized geometry by QM looks strange (it is wrong) and the topology
of your molecule is wrong also (I think); that means the force field
(FF) atom types are wrong and consequently many unknown FF parameters
showed up in the frcmod.unknown file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFmyR4WopAADFKhpZR2zZdRFJrMFJ2zyAWADF/P1314/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
My feeling is that if the topology of your molecule is correct, the FF
atom types should be quite simple and you should observed few unknown
FF parameters...
I hope this helps,
regards, Francois
> Dear Marcelo,leaprc.q4mdfft
> Thanks for your suggestion. I have run the R.E.D. server and then use
> the leaprc.q4mdfft script to get the topology and parameter file. But
> it gives the following error
> saveAmberParm UNK UNK.parm UNK.rst
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Could not find angle parameter: CM - OS - CB
> Could not find angle parameter: OS - CB - CT
> Could not find angle parameter: CT - CB - CT
> Could not find angle parameter: OH - CT - CB
> Could not find angle parameter: OH - CT - CB
> Could not find angle parameter: OS - CB - CT
> Could not find angle parameter: OS - CB - CA
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CB - CT - OH
> Could not find angle parameter: CM - CT - CM
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CM - CB - CM
> Could not find angle parameter: CM - CT - OH
> Could not find angle parameter: CM - CT - CB
> Could not find angle parameter: CB - CA - CM
> Could not find angle parameter: CB - CT - OH
> Could not find angle parameter: HA - CA - CM
> Could not find angle parameter: CT - CB - CT
> Could not find angle parameter: CB - CT - OH
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CB - CT - OH
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: CT - CB - CT
> Could not find angle parameter: OH - CT - CB
> Could not find angle parameter: CM - OS - CB
> Could not find angle parameter: CB - CT - OH
> Could not find angle parameter: CB - CT - CB
> Could not find angle parameter: OH - CT - CB
> Could not find angle parameter: OH - CT - CB
> Building proper torsion parameters.
> 1-4: angle 3 28 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 3 27 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 7 11 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 7 10 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 9 48 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 9 47 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 10 11 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 27 28 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 47 48 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> ** No torsion terms for CM-OS-CB-CT
> ** No torsion terms for CM-OS-CB-CB
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for OS-CT-CT-CM
> ** No torsion terms for OS-CT-CT-CM
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for CM-CT-CT-OS
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for CM-CT-OS-CT
> ** No torsion terms for OS-CB-CT-H1
> ** No torsion terms for OS-CB-CT-OH
> ** No torsion terms for OS-CB-CT-CB
> ** No torsion terms for CT-CT-CB-CB
> ** No torsion terms for CT-CT-CB-CB
> ** No torsion terms for CT-CT-CB-CA
> ** No torsion terms for CT-CT-CB-CT
> ** No torsion terms for CT-OS-CT-CB
> ** No torsion terms for CT-OS-CT-CB
> ** No torsion terms for H1-CT-CT-CB
> ** No torsion terms for H1-CT-CT-CB
> ** No torsion terms for H1-CT-OS-CT
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CT-CM
> ** No torsion terms for OS-CT-CB-CT
> ** No torsion terms for OS-CT-CB-CM
> ** No torsion terms for CT-CB-CT-CT
> ** No torsion terms for CT-CB-CT-OH
> ** No torsion terms for CT-CB-CT-CT
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CT-CB
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for OS-CT-CB-CB
> ** No torsion terms for OS-CT-CB-CA
> ** No torsion terms for OS-CT-CB-CT
> ** No torsion terms for CT-CB-CM-HA
> ** No torsion terms for H1-CT-CB-CB
> ** No torsion terms for H1-CT-CB-CM
> ** No torsion terms for H1-CT-CB-CB
> ** No torsion terms for OH-CT-CB-CB
> ** No torsion terms for OH-CT-CB-CM
> ** No torsion terms for OH-CT-CB-CB
> ** No torsion terms for OS-CM-CB-CT
> ** No torsion terms for OS-CM-CB-CT
> ** No torsion terms for OS-CB-CT-CB
> ** No torsion terms for OS-CB-CT-CB
> ** No torsion terms for OS-CB-CT-OH
> ** No torsion terms for CB-CT-CB-CM
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CT-CB-CA
> ** No torsion terms for CB-CT-CB-CT
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CM-CT-OS-CT
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for HA-CM-CB-CB
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CM-CT
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CT-OS-CT
> ** No torsion terms for CB-CT-CT-CM
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CB-CT-CT
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CM-CT-OS-CT
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for CM-CM-CB-CB
> ** No torsion terms for CM-CM-CB-CM
> ** No torsion terms for HA-CM-CM-CB
> ** No torsion terms for CT-OS-CT-CB
> ** No torsion terms for CT-CM-CM-CB
> ** No torsion terms for CT-CT-CB-CB
> ** No torsion terms for CT-CT-CB-CB
> ** No torsion terms for CT-CT-CB-CB
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CB-CM-HA
> ** No torsion terms for CB-CB-CM-CT
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CT-CB
> ** No torsion terms for CM-CB-CM-HA
> ** No torsion terms for CM-CB-CM-CT
> ** No torsion terms for CM-CT-CB-CB
> ** No torsion terms for CM-CT-CB-CA
> ** No torsion terms for CB-CT-CT-CM
> ** No torsion terms for CA-CB-CT-CT
> ** No torsion terms for CA-CB-CT-OH
> ** No torsion terms for CA-CB-CT-CT
> ** No torsion terms for CM-CT-OS-CT
> ** No torsion terms for CM-CT-CT-H1
> ** No torsion terms for CM-CT-CT-CB
> ** No torsion terms for CT-CT-CB-CT
> ** No torsion terms for CT-CT-CB-CT
> ** No torsion terms for CT-CT-CB-CM
> ** No torsion terms for CT-CT-CT-H1
> ** No torsion terms for CT-OS-CT-H1
> ** No torsion terms for CT-OS-CT-CB
> ** No torsion terms for CT-CT-CB-CT
> ** No torsion terms for CT-CT-CB-CM
> ** No torsion terms for CT-CB-CT-CB
> ** No torsion terms for CT-CB-CT-OH
> ** No torsion terms for CT-CB-CM-H4
> ** No torsion terms for H1-CT-CB-CT
> ** No torsion terms for H1-CT-CB-CM
> ** No torsion terms for CB-CT-CB-CM
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CT-CB-CA
> ** No torsion terms for CT-CB-CT-CB
> ** No torsion terms for CT-CB-CT-OH
> ** No torsion terms for CT-CB-CT-CB
> ** No torsion terms for CT-CB-CM-H4
> ** No torsion terms for OH-CT-CB-CT
> ** No torsion terms for OH-CT-CB-CM
> ** No torsion terms for CB-CT-CB-CT
> ** No torsion terms for CM-OS-CB-CT
> ** No torsion terms for CM-OS-CB-CA
> ** No torsion terms for CB-CT-CB-CA
> ** No torsion terms for CB-CB-CT-H1
> ** No torsion terms for CB-CB-CT-OH
> ** No torsion terms for CB-CB-CA-CA
> ** No torsion terms for OH-CT-CB-CB
> ** No torsion terms for OH-CT-CB-CA
> ** No torsion terms for CB-CT-CB-CB
> ** No torsion terms for CB-CA-CA-CB
> ** No torsion terms for HA-CA-CA-CB
> ** No torsion terms for H1-CT-CB-CA
> ** No torsion terms for OH-CT-CB-CA
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for OS-CT-CB-CB
> atoms are: O2 C5 C6 C7
> ** Warning: No sp2 improper torsion term for CT-CB-CB-CB
> atoms are: C4 C6 C7 C8
> ** Warning: No sp2 improper torsion term for CB-CB-CB-CT
> atoms are: C7 C11 C8 C24
> ** Warning: No sp2 improper torsion term for CT-CM-CB-CB
> atoms are: C5 C9 C10 C11
> ** Warning: No sp2 improper torsion term for CB-CB-CB-CB
> atoms are: C8 C10 C11 C12
> ** Warning: No sp2 improper torsion term for CB-CT-CB-CB
> atoms are: C11 C15 C12 C28
> ** Warning: No sp2 improper torsion term for CT-CB-CB-CB
> atoms are: C15 C18 C16 C32
> ** Warning: No sp2 improper torsion term for CB-CM-CB-CM
> atoms are: C16 C17 C18 C19
> ** Warning: No sp2 improper torsion term for CT-CA-CB-CT
> atoms are: C4 C21 C20 C25
> ** Warning: No sp2 improper torsion term for CB-CT-CB-CT
> atoms are: C12 C29 C28 C33
> ** Warning: No sp2 improper torsion term for CT-CT-CB-CM
> atoms are: C27 C29 C30 C31
> ** Warning: No sp2 improper torsion term for CB-CT-CB-CB
> atoms are: C16 C33 C32 C37
> ** Warning: No sp2 improper torsion term for OS-CT-CB-CA
> atoms are: O5 C33 C34 C35
> ** Warning: No sp2 improper torsion term for CB-CT-CB-CA
> atoms are: C32 C36 C37 C38
> --Impropers:
> 1 C18<UNK> - H19<UNK> - C19<UNK> - C36<UNK>
> 1 C1<UNK> - H11<UNK> - C2<UNK> - C3<UNK>
> 1 C20<UNK> - H16<UNK> - C21<UNK> - C22<UNK>
> 1 C21<UNK> - H8<UNK> - C22<UNK> - C23<UNK>
> 1 C22<UNK> - H15<UNK> - C23<UNK> - C26<UNK>
> 1 C34<UNK> - H12<UNK> - C35<UNK> - C38<UNK>
> 1 H10<UNK> - C2<UNK> - C1<UNK> - O2<UNK>
> 1 H21<UNK> - C14<UNK> - C13<UNK> - C17<UNK>
> 1 H22<UNK> - C10<UNK> - C9<UNK> - C14<UNK>
> 1 O5<UNK> - C30<UNK> - C31<UNK> - H13<UNK>
> total 10 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
> Here I am attaching the script , mol2 file and the force field files.
> Please help me.
>
> On Wed, Mar 9, 2016 at 6:10 PM, Marcelo Andrade Chagas
> <andrade.mchagas.gmail.com> wrote:
>> Hi
>>
>> you have tried to get by this server?
>>
>> Currently has the most widely used acid and fast
>>
>> Best regards
>>
>> http://upjv.q4md-forcefieldtools.org/RED/
>>
>> I will create a tutorial in the coming days if you have time,
>>
>> and available on the page of my collaboration group.
>>
>> Try to see examples
>>
>> Marcelo
>>
>> Marcelo Andrade Chagas, MSc
>> (PhD student)
>> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
>> * http://lqcmm.qui.ufmg.br/
>> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
>> Tel:(31)3409-5776
>>
>> 2016-03-09 5:36 GMT-03:00 Jesmita Dhar <dhar.beauty.gmail.com>:
>>
>>> Dear sir/madam,
>>> I want to create a parameter file for graphene oxide. But due to its
>>> huge structure antechember can not create the paramater file. So we
>>> select a unit from the graphene oxide. The selected unit would be
>>> optimized in gaussian with RESP prereq as I want to use the gaussian
>>> output to get RESP charges and Gaff atom types in ANTECHEMBER. I have
>>> run optimization in gaussian 09 software. But can not able to calculte
>>> RESP. Is it possible to get RESP charge from antechember? If yes, what
>>> should be command.Here I am attaching the optimized pdb file of
>>> graphene oxide. Please help..
>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Fri Mar 11 2016 - 05:00:08 PST
