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