Re: [AMBER] frcmod file error from Thakur, Abhishek on 2016-10-20 (Amber Archive Oct 2016)

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 20 Oct 2016 16:29:19 +0000

I am sorry Dr.Carlos for disturbing you during working hours.

In my leap file there seems to be no error and but still structure is linear

________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, October 20, 2016 5:14:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] frcmod file error

that doesn't make sense.
as I said before, generating a clean leap.log file and looking at what leap
says it is doing may help you.

On Thu, Oct 20, 2016 at 11:59 AM, Thakur, Abhishek <axt651.miami.edu> wrote:

> 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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> > 8SN5Q89lVTcSAFz0940JNz3RzCCPs&
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> > > > 0Hah93XWYYBgmROOVcaccg&m=jbzG8RFnibcn6VYCd16zuRwF8ZQKF_
> > > > brz7oG1zbD7Jc&s=Pec7P_U0dS67_QGlaK_7WrvmaUwplPhrtsDmcCBCnVc&e=
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> > > > brz7oG1zbD7Jc&s=Pec7P_U0dS67_QGlaK_7WrvmaUwplPhrtsDmcCBCnVc&e=
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> > > IFT45uprhvkuI&s=AAg-IY7xfhG6eO4b3Me4Hr_MtlAf35PhOtcDH9V4Pm8&e=
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application/octet-stream attachment: leap.log

chemical/x-pdb attachment: peptide.pdb

Received on Thu Oct 20 2016 - 10:00:02 PDT