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<P><FONT SIZE=2>Hi David,<BR>
<BR>
Thanks for your reply. I tried removing the 2nd H to OG. Still, giving me same error and segmentation fault.<BR>
<BR>
With regards,<BR>
<BR>
Abu<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
Sent: Tue 9/6/2005 11:58 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] Segmentation fault<BR>
<BR>
On Tue, 2005-09-06 at 11:13 +0100, Naser, Md Abu wrote:<BR>
> Hi All,<BR>
><BR>
> I have included a new amino acid- phosphoserine(PSE) in rtp file.<BR>
> Although,I included the amino acid in ffG43a1.hdb and<BR>
><BR>
> pdb2gmx -f xxx.pdb -o xxx.gro -ignh -missing -p xxx.top, gives<BR>
><BR>
> WARNING: atom H is missing in residue PSE 67 in the pdb file<BR>
> You might need to add atom H to the hydrogen database of<BR>
> residue PSE<BR>
> in the file ff???.hdb<BR>
><BR>
> When I run mdrun, i am getting segmentation fault.<BR>
><BR>
><BR>
> Can anyone advise me where might be problem?<BR>
You should remove the second H (to OG) from the hdb file, since it is<BR>
not there anymore.<BR>
<BR>
><BR>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>
> in ffG43a1.rtp<BR>
> [ PSE ]<BR>
><BR>
> [ atoms ]<BR>
> N N -0.28000 0<BR>
> H H 0.28000 0<BR>
> CA CH1 0.00000 1<BR>
> CB CH2 0.15000 2<BR>
> OG OA -0.54800 2<BR>
> P P 0.79800 2<BR>
> O1P OM -0.80000 2<BR>
> O2P OM -0.80000 2<BR>
> O3P OM -0.80000 2<BR>
> C C 0.380 3<BR>
> O O -0.380 3<BR>
> [ bonds ]<BR>
> N H gb_2 <BR>
> N CA gb_20 <BR>
> CA C gb_26 <BR>
> C O gb_4 <BR>
> C +N gb_9 <BR>
> CA CB gb_26 <BR>
> CB OG gb_17 <BR>
> P O1P ga_23<BR>
> P O2P ga_23<BR>
> P O3P ga_23<BR>
> P OG ga_27<BR>
> [ angles ]<BR>
> ; ai aj ak gromos type<BR>
> -C N H ga_31 <BR>
> H N CA ga_17 <BR>
> -C N CA ga_30 <BR>
> N CA C ga_12 <BR>
> CA C +N ga_18 <BR>
> CA C O ga_29 <BR>
> O C +N ga_32 <BR>
> N CA CB ga_12 <BR>
> C CA CB ga_12 <BR>
> CA CB OG ga_12<BR>
> OG P O1P ga_23<BR>
> OG P O2P ga_23<BR>
> OG P O3P ga_23<BR>
> CB OG P ga_27<BR>
> O1P P O2P ga_28<BR>
> O1P P O3P ga_28<BR>
> O2P P O3P ga_28<BR>
> [ impropers ]<BR>
> ; ai aj ak al gromos type<BR>
> N -C CA H gi_1 <BR>
> C CA +N O gi_1 <BR>
> CA N C CB gi_2 <BR>
> [ dihedrals ]<BR>
> ; ai aj ak al gromos type<BR>
> -CA -C N CA gd_4 <BR>
> -C N CA C gd_19 <BR>
> N CA C +N gd_20 <BR>
> N CA CB OG gd_17 <BR>
> CA CB OG P gd_12<BR>
> CB OG P O1P gd_11<BR>
> CB OG P O2P gd_11<BR>
> CB OG P O3P gd_11<BR>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>
> in ffG43a1.hdb<BR>
> PSE 2<BR>
> 1 1 N -C CA <BR>
> 1 2 OG CB CA<BR>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>
><BR>
><BR>
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--<BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</A><BR>
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