Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server

From: Cecilia Lindgren <cecilia.lindgren.umu.se>
Date: Thu, 18 Aug 2016 06:11:15 +0000

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 Wed Aug 17 2016 - 23:30:02 PDT
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