> There is no "CT-NT-P-OS"
Did you possibly typo the order on "CT - OS - P - NT" for example?
If you see CT-NT-P-OS in the frcmod, please paste the contents of the
file into email to verify it. Either there is some misapprehension about
format, or you may have found a bug.
Bill
On 8/18/16 2:03 AM, Cecilia Lindgren wrote:
> There is no "CT-NT-P-OS" or "OS-P-NT-CT" in the outout (I include it below)
>
> Best,
> Cecilia
>
>> desc parm
> PARMSET
> --Atoms
> C Mass= 12.01 Polar= 0.62 E = 0.09 R= 1.91
> Element=C Hybrid= Sp2 Desc:
> CT Mass= 12.01 Polar= 0.88 E = 0.11 R= 1.91
> Element=C Hybrid= Sp3 Desc:
> H Mass= 1.01 Polar= 0.16 E = 0.02 R= 0.60
> Element=H Hybrid= Sp3 Desc:
> H1 Mass= 1.01 Polar= 0.14 E = 0.02 R= 1.39
> Element=H Hybrid= Sp3 Desc:
> HC Mass= 1.01 Polar= 0.14 E = 0.02 R= 1.49
> Element=H Hybrid= Sp3 Desc:
> N Mass= 14.01 Polar= 0.53 E = 0.17 R= 1.82
> Element=N Hybrid= Sp2 Desc:
> NT Mass= 14.01 Polar= 0.53 E = 0.17 R= 1.82
> Element=N Hybrid= Sp3 Desc:
> O Mass= 16.00 Polar= 0.43 E = 0.21 R= 1.66
> Element=O Hybrid= Sp2 Desc:
> O2 Mass= 16.00 Polar= 0.43 E = 0.21 R= 1.66
> Element=O Hybrid= Sp2 Desc:
> OS Mass= 16.00 Polar= 0.47 E = 0.17 R= 1.68
> Element=O Hybrid= Sp3 Desc:
> P Mass= 30.97 Polar= 1.54 E = 0.20 R= 2.10
> Element=P Hybrid= Sp3 Desc:
> --Bonds
> C - CT Kb= 315.00 R0= 1.52 Desc:
> C - N Kb= 490.00 R0= 1.33 Desc:
> C - O Kb= 570.00 R0= 1.23 Desc:
> CT - CT Kb= 310.00 R0= 1.53 Desc:
> CT - H1 Kb= 340.00 R0= 1.09 Desc:
> CT - HC Kb= 340.00 R0= 1.09 Desc:
> CT - N Kb= 335.00 R0= 1.45 Desc:
> CT - NT Kb= 365.00 R0= 1.47 Desc:
> CT - OS Kb= 320.00 R0= 1.41 Desc:
> H - N Kb= 435.00 R0= 1.01 Desc:
> NT - P Kb= 375.00 R0= 1.66 Desc:
> O2 - P Kb= 525.00 R0= 1.48 Desc:
> OS - P Kb= 230.00 R0= 1.61 Desc:
> --Angles
> CT - C - N Kt= 70.00 T0= 116.60 Desc:
> CT - C - O Kt= 80.00 T0= 120.40 Desc:
> N - C - O Kt= 80.00 T0= 122.90 Desc:
> C - CT - CT Kt= 65.00 T0= 111.10 Desc:
> C - CT - H1 Kt= 50.00 T0= 109.50 Desc:
> C - CT - HC Kt= 50.00 T0= 109.50 Desc:
> C - CT - N Kt= 65.00 T0= 110.10 Desc:
> CT - CT - H1 Kt= 50.00 T0= 109.50 Desc:
> CT - CT - HC Kt= 50.00 T0= 109.50 Desc:
> CT - CT - N Kt= 80.00 T0= 109.70 Desc:
> CT - CT - OS Kt= 50.00 T0= 109.50 Desc:
> H1 - CT - H1 Kt= 35.00 T0= 109.50 Desc:
> H1 - CT - N Kt= 50.00 T0= 109.50 Desc:
> H1 - CT - NT Kt= 50.00 T0= 109.50 Desc:
> H1 - CT - OS Kt= 50.00 T0= 109.50 Desc:
> HC - CT - HC Kt= 35.00 T0= 109.50 Desc:
> C - N - CT Kt= 50.00 T0= 121.90 Desc:
> C - N - H Kt= 50.00 T0= 120.00 Desc:
> CT - N - H Kt= 50.00 T0= 118.04 Desc:
> CT - NT - CT Kt= 50.00 T0= 109.50 Desc:
> CT - NT - P Kt= 80.00 T0= 119.35 Desc:
> CT - OS - P Kt= 100.00 T0= 120.50 Desc:
> NT - P - O2 Kt= 45.00 T0= 113.54 Desc:
> NT - P - OS Kt= 45.00 T0= 98.88 Desc:
> O2 - P - OS Kt= 100.00 T0= 108.23 Desc:
> OS - P - OS Kt= 45.00 T0= 102.60 Desc:
> --Torsions
> CT - CT - C - N
> Kp= 0.00 N=4 P0= 0.00 Order: 0123 Desc:
> CT - CT - C - N
> Kp= 0.40 N=3 P0= 0.00 Order: 0123 Desc:
> CT - CT - C - N
> Kp= 0.20 N=2 P0= 0.00 Order: 0123 Desc:
> CT - CT - C - N
> Kp= 0.20 N=1 P0= 0.00 Order: 0123 Desc:
> H1 - CT - C - N
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> HC - CT - C - N
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> N - C - CT - N
> Kp= 0.00 N=4 P0= 0.00 Order: 0123 Desc:
> N - C - CT - N
> Kp= 0.55 N=3 P0= 180.00 Order: 0123 Desc:
> N - C - CT - N
> Kp= 1.58 N=2 P0= 180.00 Order: 0123 Desc:
> N - C - CT - N
> Kp= 0.45 N=1 P0= 180.00 Order: 0123 Desc:
> CT - CT - C - O
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> H1 - CT - C - O
> Kp= 0.80 N=1 P0= 0.00 Order: 0123 Desc:
> H1 - CT - C - O
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> H1 - CT - C - O
> Kp= 0.08 N=3 P0= 180.00 Order: 0123 Desc:
> HC - CT - C - O
> Kp= 0.80 N=1 P0= 0.00 Order: 0123 Desc:
> HC - CT - C - O
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> HC - CT - C - O
> Kp= 0.08 N=3 P0= 180.00 Order: 0123 Desc:
> N - CT - C - O
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> CT - C - N - CT
> Kp= 2.50 N=2 P0= 180.00 Order: 0123 Desc:
> CT - C - N - H
> Kp= 2.50 N=2 P0= 180.00 Order: 0123 Desc:
> CT - N - C - O
> Kp= 2.50 N=2 P0= 180.00 Order: 0123 Desc:
> H - N - C - O
> Kp= 2.50 N=2 P0= 180.00 Order: 0123 Desc:
> H - N - C - O
> Kp= 2.00 N=1 P0= 0.00 Order: 0123 Desc:
> C - CT - CT - H1
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> C - CT - CT - OS
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - CT - H1
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - CT - HC
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - CT - N
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - CT - OS
> Kp= 0.00 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - CT - OS
> Kp= 0.25 N=1 P0= 0.00 Order: 0123 Desc:
> HC - CT - CT - OS
> Kp= 0.00 N=3 P0= 0.00 Order: 0123 Desc:
> HC - CT - CT - OS
> Kp= 0.25 N=1 P0= 0.00 Order: 0123 Desc:
> N - CT - CT - OS
> Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc:
> C - CT - N - C
> Kp= 0.00 N=4 P0= 0.00 Order: 0123 Desc:
> C - CT - N - C
> Kp= 0.42 N=3 P0= 0.00 Order: 0123 Desc:
> C - CT - N - C
> Kp= 0.27 N=2 P0= 0.00 Order: 0123 Desc:
> C - CT - N - C
> Kp= 0.00 N=1 P0= 0.00 Order: 0123 Desc:
> C - CT - N - H
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> C - N - CT - CT
> Kp= 0.00 N=4 P0= 0.00 Order: 0123 Desc:
> C - N - CT - CT
> Kp= 0.40 N=3 P0= 0.00 Order: 0123 Desc:
> C - N - CT - CT
> Kp= 2.00 N=2 P0= 0.00 Order: 0123 Desc:
> C - N - CT - CT
> Kp= 2.00 N=1 P0= 0.00 Order: 0123 Desc:
> CT - CT - N - H
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> C - N - CT - H1
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> H - N - CT - H1
> Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc:
> CT - NT - CT - H1
> Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - NT - P
> Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc:
> CT - CT - OS - P
> Kp= 0.38 N=3 P0= 0.00 Order: 0123 Desc:
> H1 - CT - OS - P
> Kp= 0.38 N=3 P0= 0.00 Order: 0123 Desc:
> CT - NT - P - O2
> Kp= 3.00 N=2 P0= 180.00 Order: 0123 Desc:
> CT - NT - P - O2
> Kp= 0.30 N=2 P0= 180.00 Order: 0123 Desc:
> CT - OS - P - NT
> Kp= 0.25 N=3 P0= 0.00 Order: 0123 Desc:
> CT - OS - P - O2
> Kp= 0.25 N=3 P0= 0.00 Order: 0123 Desc:
> CT - OS - P - OS
> Kp= 0.25 N=3 P0= 0.00 Order: 0123 Desc:
> CT - OS - P - OS
> Kp= 1.20 N=2 P0= 0.00 Order: 0123 Desc:
> --Impropers
> CT - N - C - O
> Kp= 10.50 N=2 P0= 180.00 Order: 0123 Desc:
> C - CT - N - H
> Kp= 1.10 N=2 P0= 180.00 Order: 0123 Desc:
> --HBonds
> --None
> --Nonbonded Edits
> --None
>
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: Bill Ross [mailto:ross.cgl.ucsf.edu]
> Sent: den 18 augusti 2016 10:50
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server
>
> Please try 'desc parm' and see if your torsion terms are visible.
>
> Bill
>
> parm = loadamberparams frcmod.known
> Loading parameters: ./frcmod.known
> Reading force field modification type file (frcmod) Reading title:
> Fvisor' for the dihedral termsRCMOD file generated by PyRED version
> SEP-2015 - q4md-forcefieldtools.org
>
>
> On 8/17/16 11:11 PM, Cecilia Lindgren wrote:
>> Thank you for your reply.
>>
>> The commands I have given are:
>>
>> tleap -f leaprc.ff99SB
>> parm = loadamberparams frcmod.known
>> F02 = loadmol2 F02.mol2
>> p = loadpdb protein.pdb
>>> bond p.69.SG p.96.SG
>>> bond p.257.SG p.272.SG
>>> bond p.409.SG p.529.S
>> saveamberparm protein.prmtop protein.inpcrd
>>
>> There are no errors after loading frcmod.known in leap.log. Later on, when I try to save the .prmtop and .inpcrd I get some warnings that says:
>>
>> Building improper torsion parameters.
>> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
>> atoms are: CG CE2 CD2 CE3
>> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
>> atoms are: NE1 CZ2 CE2 CD2
>> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
>> atoms are: CG CE2 CD2 CE3
>>
>> and so on. I attach the file.
>>
>>
>> Best regards,
>> Cecilia
>>
>> -----Original Message-----
>> From: David A Case [mailto:david.case.rutgers.edu]
>> Sent: den 17 augusti 2016 16:14
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server
>>
>> On Wed, Aug 17, 2016, Cecilia Lindgren wrote:
>>> Building proper torsion parameters.
>>> ** No torsion terms for CT-NT-P-OS
>>> ** No torsion terms for CT-NT-P-OS
>>> ** No torsion terms for OS-P-NT-CT
>>> ** No torsion terms for OS-P-NT-CT
>>>
>>> I am using ff99SB. There were some bonds, angles and dihedrals missing
>>> when parameterizing, but I have used the analogous parameters from the
>>> gaff force field, and received an frcmod file which I have uploaded,
>>> and amber is not complaining about any other of those parameters. (One
>>> of these that I have in the frcmod file is CT-NT-P-OS). I have
>>> attached the frcmod.known file that I have used.
>> Can you list the exact commands you gave to tleap? Have you carefully examined the leap.log file to see there are any messages relating the "loadAmberParams frcmod.known" command?
>>
>> ...dac
>>
>>
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>>
>>
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Received on Thu Aug 18 2016 - 02:30:03 PDT
