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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Received on Thu Aug 18 2016 - 02:00:07 PDT
