It is not working.
It is unable to join N-C terminal for me.
Structure breaks in 3-4 parts
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, October 20, 2016 4:39:43 AM
To: AMBER Mailing List
Subject: Re: [AMBER] frcmod file error
if you tell Leap the sequence, you must also tell it that you want to make
it cyclic by bonding the first to last amino acid. Otherwise it has no idea
you want to do that. You can use the bond command.
On Thu, Oct 20, 2016 at 11:35 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> I have just used leap to make linear peptide from one letter sequence.
>
> Then while trying to make it cyclic the structure was breaking apart.
>
> So I have found a served which did for me.
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__osddlinux.osdd.net_raghava_pepstrmod_cyc-5Fss.php&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=xMOUeGBJH4wLb7o61LHRexcoGMrUX221ZIxyOTfQXMs&s=c9Id5qUsEekAU1xMmCxEjZEqXPShO7HBVwKkRV4d2Rg&e=
>
>
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__osddlinux.osdd.net_raghava_pepstrmod_cyc-5Fss.php&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=xMOUeGBJH4wLb7o61LHRexcoGMrUX221ZIxyOTfQXMs&s=c9Id5qUsEekAU1xMmCxEjZEqXPShO7HBVwKkRV4d2Rg&e= >
>
> But still it could not bond N-C so I have done it manually
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__osddlinux.osdd.net_raghava_pepstrmod_cyc-5Fss.php&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=xMOUeGBJH4wLb7o61LHRexcoGMrUX221ZIxyOTfQXMs&s=c9Id5qUsEekAU1xMmCxEjZEqXPShO7HBVwKkRV4d2Rg&e= >
>
> PEPstrMOD: Peptide Tertiary Structure Prediction with ...<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__osddlinux.osdd.net_raghava_pepstrmod_cyc-5Fss.php&d=DQICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=xMOUeGBJH4wLb7o61LHRexcoGMrUX221ZIxyOTfQXMs&s=c9Id5qUsEekAU1xMmCxEjZEqXPShO7HBVwKkRV4d2Rg&e= >
> osddlinux.osdd.net
> This page is designed to predict the peptide structure with N-to-C
> terminal cyclization. The peptide is made cyclic by incorporating a bond
> between Nitrogen atom of N ...
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Thursday, October 20, 2016 4:26:51 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] frcmod file error
>
> it looks to me that Leap doesn't understand that you want to bond the first
> amino acid to the last, and it assigns the N3 atom type to the Glu1
> backbone N. Later it has them connected, so it looks for a bond of that
> type but doesn't find it because the N3 is not the right atom type for a
> backbone amide.
>
> I haven't done any cyclic peptides like this, maybe someone else on the
> list might have done it. You can also send your leap log file, it may have
> helpful info. MAKE SURE TO DELETE THE LOG FILE, THEN RERUN ONLY THIS
> SCRIPT. otherwise the log file will have info from all of your attempts.
>
>
> On Thu, Oct 20, 2016 at 11:04 AM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Sorry Dr.carlos,
> >
> > I have a written tutorial, So I have copy pasted it. Just to show how I
> > have proceeded
> >
> >
> >
> > > tleap -s -f leaprc.ff14SB
> >
> > > source leaprc.gaff
> >
> > >peptide = loadpdb 2.pdb
> >
> > > solvate peptide TIP3PBOX 10>
> >
> > >charge peptide
> >
> > > addIons peptide Na+ 2
> >
> > > loadAmberParams frcmod.ionsjc_tip3p
> >
> > > saveamberparm peptide peptide.prmtop peptide.inpcrd
> >
> >
> >
> > This is what I have done,
> >
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Thursday, October 20, 2016 3:54:36 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] frcmod file error
> >
> > I find the things you are saying to be confusing. You sent a pdb file
> > (2.pdb) that has only normal amino acids and should work fine, but then
> in
> > your email you don't show that this is the pdb file that you used for
> Leap.
> > Also this is just a peptide, so why would you save the files as
> "complex"?
> >
> > What error do you get if you try to use only the pdb file that you sent?
> If
> > no error, then what is the pdb file that gives you the error? I still
> don't
> > see anything in what you sent that explains why you are trying to use
> gaff.
> >
> > On Thu, Oct 20, 2016 at 10:46 AM, Thakur, Abhishek <axt651.miami.edu>
> > wrote:
> >
> > > yes I have tried that
> > >
> > >
> > > What I did was
> > >
> > > > > source leaprc.gaff
> > > > > loadamberparams PLX4720.frcmod
> > > > > solvateBox complex TIP3PBOX 10
> > > > > charge complex
> > > > > addIons complex Cl- 7
> > > > > saveamberparm complex V600E_4720.prmtop V600E_4720.inpcrd
> > >
> > >
> > > and it gave me following error
> > >
> > > For your reference I have attached my pdb file
> > >
> > >
> > > That is why I was trying to make frcmod file as it is asking me those
> > > parameters
> > >
> > >
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > > Sent: Thursday, October 20, 2016 3:40:39 AM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] frcmod file error
> > >
> > > if it is standard amino acids, I'm not sure I understand why you are
> > using
> > > a frcmod file.. Did you try without it?
> > >
> > > On Thu, Oct 20, 2016 at 10:37 AM, Thakur, Abhishek <axt651.miami.edu>
> > > wrote:
> > >
> > > > Hey Dr.David,
> > > >
> > > >
> > > > Thank you for your suggestion, I think I have a cyclic peptide of
> > around
> > > > 75 atoms, so I think that is why antechamber is not working.
> > > >
> > > >
> > > > So I tried making it as protein is prepared. As I just want to
> simulate
> > > > this peptide by solvating it, so I have not frcmod, lib files of
> > > heteroatom
> > > > to load.
> > > >
> > > > So as these are peptide amber should build it as a protein? No hetero
> > > atom
> > > > only small chain of 9 amino acid in cyclic form.
> > > >
> > > >
> > > > > source leaprc.gaff
> > > > > loadamberparams PLX4720.frcmod
> > > > > solvateBox complex TIP3PBOX 10
> > > > > charge complex
> > > > > addIons complex Cl- 7
> > > > > saveamberparm complex V600E_4720.prmtop V600E_4720.inpcrd
> > > >
> > > >
> > > > The error that I am getting is
> > > >
> > > >
> > > > Could not find bond parameter for: N3 - C
> > > > Building angle parameters.
> > > > Could not find angle parameter: CX - N3 - C
> > > > Could not find angle parameter: H - N3 - C
> > > > Could not find angle parameter: H - N3 - C
> > > > Could not find angle parameter: H - N3 - C
> > > > Could not find angle parameter: N3 - C - CX
> > > > Could not find angle parameter: N3 - C - O2
> > > > Could not find angle parameter: N3 - C - O2
> > > > Building proper torsion parameters.
> > > > ** No torsion terms for CX-N3-C-CX
> > > > ** No torsion terms for CX-N3-C-O2
> > > > ** No torsion terms for CX-N3-C-O2
> > > > ** No torsion terms for H-N3-C-CX
> > > > ** No torsion terms for H-N3-C-O2
> > > > ** No torsion terms for H-N3-C-O2
> > > > ** No torsion terms for H-N3-C-CX
> > > > ** No torsion terms for H-N3-C-O2
> > > > ** No torsion terms for H-N3-C-O2
> > > > ** No torsion terms for H-N3-C-CX
> > > > ** No torsion terms for H-N3-C-O2
> > > > ** No torsion terms for H-N3-C-O2
> > > >
> > > >
> > > > As antechamber doe not work so I am unable to generate frcmod file
> > > > containing this files.
> > > >
> > > > But as these are just amino acid do I need to give frcmod file or lib
> > for
> > > > these things?
> > > >
> > > > If yes then how do I generate it as antechamber is not creating a
> mol2
> > > > file for my peptide and amber gives error if I use mol2 file
> generated
> > by
> > > > some other software and make frcmod file.
> > > >
> > > > Unknown keyword: C.3-C.3-S. in parameter file. Perhaps a format
> error?
> > > >
> > > >
> > > >
> > > > Thanking you,
> > > >
> > > > Abhsihek
> > > >
> > > >
> > > > ________________________________
> > > > From: David A Case <david.case.rutgers.edu>
> > > > Sent: Wednesday, October 19, 2016 1:06:36 PM
> > > > To: AMBER Mailing List
> > > > Subject: Re: [AMBER] frcmod file error
> > > >
> > > > On Wed, Oct 19, 2016, Thakur, Abhishek wrote:
> > > > >
> > > > > > antechamber -i PLX4720.pdb -fi pdb -o PLX4720.mol2 -fo mol2 -c
> bcc
> > > -s 2
> > > > > But It was continuously giving me error
> > > >
> > > > > ---Judge bond type for Residue 1 with ID of 1 and Name of GLU ---
> > > > >
> > > > > ---Judge bond type for Residue 2 with ID of 2 and Name of ASN ---
> > > > >
> > > > > Warning: the assigned bond types may be wrong, please :
> > > > > (1) double check the structure (the connectivity) and/or
> > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or
> > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c
> > > > > Be cautious, use a large value of PSCUTOFF (>100) will
> > > significantly
> > > > increase the computation time
> > > >
> > > > Note: antechamber is intended for *small molecules*, not for
> > polypeptides
> > > > or
> > > > proteins. Amber builds proteins in a completely different way:
> please
> > > see
> > > > the
> > > > manual or tutorials.
> > > >
> > > > [Scott: does acdoctor properly complain if a user tries to use a
> > protein
> > > > pdb
> > > > file?]
> > > >
> > > > ...good luck...dac
> > > >
> > > >
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Received on Thu Oct 20 2016 - 09:00:04 PDT
