[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)
Jignesh Patel
jbp087 at gmail.com
Mon Nov 29 07:47:33 CET 2010
Dear Justin,
Thanks for your reply.
I have checked whole pdb file. Everything is fine.
When I remove phosphorylated serine and use only serine then every thing
went fine.
co-ordinates for phosphoserine are as per following
ATOM 1684 N SEP X 167 27.040 22.580 8.280 1.00
0.00
ATOM 1685 H SEP X 167 27.150 23.470 7.820 1.00
0.00
ATOM 1686 CA SEP X 167 28.020 22.270 9.340 1.00
0.00
ATOM 1687 CB SEP X 167 29.330 21.760 8.740 1.00
0.00
ATOM 1688 OG SEP X 167 30.210 21.300 9.770 1.00
0.00
ATOM 1689 P SEP X 167 29.763 21.418 10.657 0.80 0.00
ATOM 1690 O1P SEP X 167 30.228 20.602 11.000 0.80
0.00
ATOM 1691 O2P SEP X 167 29.298 22.234 10.314 0.80
0.00
ATOM 1692 O3P SEP X 167 29.316 21.536 11.544 0.80 0.00
ATOM 1693 C SEP X 167 28.320 23.540 10.140 1.00
0.00
ATOM 1694 O SEP X 167 28.980 24.460 9.660 1.00 0.00
and following details regarding the error,
Identified residue MET1 as a starting terminus.
Warning: Residue SEP167 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ASN168 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue PHE169 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ALA170 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue VAL171 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue GLN166 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 HIS122 CYS127 MET155 HIS181 CYS232
SD5 NE2953 SG987 SD1198 NE21417 SG1802
HIS122 NE2953 0.896
CYS127 SG987 2.406 2.338
MET155 SD1198 2.631 2.424 0.726
HIS181 NE21417 2.143 2.161 2.124 1.774
CYS232 SG1802 2.805 3.428 3.766 3.748 2.309
HIS273 NE22097 4.614 4.982 4.609 4.323 3.017 2.266
Start terminus: NH3+
End terminus: COO-
Checking for duplicate atoms....
Now there are 283 residues with 2821 atoms
Making bonds...
Number of bonds was 2866, now 2861
Generating angles, dihedrals and pairs...
Before cleaning: 4579 pairs
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.5.1
Source code file: pgutil.c, line: 88
Fatal error:
Atom N not found in residue seq.nr. 1 while adding improper
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanking you.
With regards,
Jignesh Patel
On Sat, Nov 27, 2010 at 4:30 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)
> 2. Re: Free Energy Calculation: dVpot/dlambda is always zero
> (Anirban Ghosh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 26 Nov 2010 22:48:22 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Error while using forcefield GROMOS 43a1p
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CF07F86.8030501 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Jignesh Patel wrote:
> > Dear Justin,
> >
> > I am trying to do simulation of a system which contains phosphorylated
> > serine using GROMOS 43a1p forcefield. While running pdb2gmx command, I
> > am getting following error.
> > Fatal error:
> > Atom N not found in residue seq.nr <http://seq.nr>. 1 while adding
> improper
> >
>
> Well, either the N atom of residue 1 is not present in your .pdb file (in
> which
> case you've got a broken structure that needs fixing), or something else is
> going on. Without seeing the contents of your input coordinate file (just
> the
> first residue, really) and your pdb2gmx command line, there's not much help
> anyone can give you.
>
> -Justin
>
> > thank you in anticipation.
> >
> > With regards,
> > Jignesh Patel
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 27 Nov 2010 13:08:41 +0530
> From: Anirban Ghosh <reach.anirban.ghosh at gmail.com>
> Subject: Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is
> always zero
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTin-7WixVZ=kcNj8r_j_dwctb8auLsFY=vKOmCSe at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Justin,
>
> Thanks a lot for the reply.
> Yes, I am using GROAMCS 4.5 and my system consists of two chains of two
> proteins, a substrate and an inhibitor solvated in water. So can you please
> tell me what should be the values for:
> couple-moltypecouple-lambda0couple-intramolThanks a lot again.
>
>
> Regards,
>
> Anirban
>
> On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > Anirban Ghosh wrote:
> >
> >>
> >> Hi ALL,
> >>
> >> I am trying to run free energy calculation and for that in the md.mdp
> file
> >> I am keeping the following option:
> >>
> >> ; Free energy control stuff
> >> free_energy = yes
> >> init_lambda = 0.0
> >> delta_lambda = 0
> >> sc_alpha =0.5
> >> sc-power =1.0
> >> sc-sigma = 0.3
> >>
> >>
> >> But still I find that in my log file the values for dVpot/dlambda is
> >> always coming to be zero.
> >> What I am doing wrong?
> >> Any suggestion is welcome. Thanks a lot in advance.
> >>
> >>
> > You haven't indicated your Gromacs version, but assuming you're using
> > something in the 4.x series, you're not specifying the necessary
> parameters
> > to do any sort of transformation, particularly couple_lambda0 and
> > couple_lambda1. If left at their default values (vdw-q), nothing gets
> > decoupled.
> >
> > -Justin
> >
> >
> >> Regards,
> >>
> >> Anirban
> >>
> >>
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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