[gmx-users] pdb2gmx assign CSER to non-terminal serine
Justin Lemkul
jalemkul at vt.edu
Tue May 3 18:04:48 CEST 2016
On 5/3/16 12:02 PM, Zheng Ruan wrote:
> Hi Gromacs Users,
>
> I'm using pdb2gmx to process my pdb files with a phospho-tyrosine
> using amber99sb-ildn.ff. The relavant content in my pdb looks like this
> (There is a serine before phosphorylated tyrosine):
>
> ATOM 202 N SER 26 31.593 -68.669 -25.834 1.00208.96
> N
> ATOM 203 CA SER 26 32.638 -67.843 -25.302 1.00208.96
> C
> ATOM 204 C SER 26 31.995 -66.621 -24.727 1.00208.96
> C
> ATOM 205 O SER 26 30.979 -66.149 -25.232 1.00208.96
> O
> ATOM 206 CB SER 26 33.644 -67.365 -26.363 1.00208.96
> C
> ATOM 207 OG SER 26 34.330 -68.476 -26.921 1.00208.96
> O
> ATOM 208 N Y2P 27 32.567 -66.088 -23.628 1.00307.13
> N
> ATOM 209 CA Y2P 27 32.019 -64.903 -23.034 1.00307.13
> C
> ATOM 210 C Y2P 27 33.156 -64.013 -22.644 1.00307.13
> C
> ATOM 211 O Y2P 27 34.263 -64.481 -22.390 1.00307.13
> O
> ATOM 212 CB Y2P 27 31.197 -65.174 -21.762 1.00307.13
> C
> ATOM 213 CG Y2P 27 30.697 -63.861 -21.266 1.00307.13
> C
> ATOM 214 OG Y2P 27 29.295 -60.184 -19.874 1.00307.13
> O
> ATOM 215 CD1 Y2P 27 29.578 -63.285 -21.820 1.00307.13
> C
> ATOM 216 CD2 Y2P 27 31.346 -63.208 -20.242 1.00307.13
> C
> ATOM 217 CE1 Y2P 27 29.115 -62.073 -21.365 1.00307.13
> C
> ATOM 218 CE2 Y2P 27 30.887 -61.996 -19.783 1.00307.13
> C
> ATOM 219 CZ Y2P 27 29.768 -61.428 -20.343 1.00307.13
> C
> ATOM 220 P Y2P 27 29.208 -59.251 -20.980 0.00 0.00
> P
> ATOM 221 O1P Y2P 27 30.631 -58.900 -21.344 0.00 0.00
> O
> ATOM 222 O2P Y2P 27 28.565 -59.705 -22.398 0.00 0.00
> O
> ATOM 223 O3P Y2P 27 28.289 -58.144 -20.524 0.00 0.00
> O
>
> I followed the online protocol to convert the amber parameters from Bryce
> into my force field. The Y2P entry in aminoacids.rtp I add looks like this:
>
> [ Y2P ]
> [ atoms ]
> N N -0.516300 1
> H H 0.293600 2
> CA CT 0.141279 3
> HA H1 0.027982 4
> CB CT -0.251171 5
> HB1 HC 0.081930 6
> HB2 HC 0.081930 7
> CG CA 0.073446 8
> CD1 CA -0.198084 9
> HD1 HA 0.112503 10
> CE1 CA -0.254266 11
> HE1 HA 0.161606 12
> CZ C 0.477009 13
> CE2 CA -0.254266 14
> HE2 HA 0.161606 15
> CD2 CA -0.198084 16
> HD2 HA 0.112503 17
> OG OS -0.557944 18
> P P 1.380672 19
> O1P O2 -0.943550 20
> O2P O2 -0.943550 21
> O3P O2 -0.943550 22
> C C 0.536600 23
> O O -0.581900 24
> [ bonds ]
> N H
> N CA
> CA HA
> CA CB
> CA C
> CB HB1
> CB HB2
> CB CG
> CG CD1
> CG CD2
> CD1 HD1
> CD1 CE1
> CE1 HE1
> CE1 CZ
> CZ OG
> CZ CE2
> CE2 HE2
> CE2 CD2
> CD2 HD2
> OG P
> P O1P
> P O2P
> C O
> -C N
> [ impropers ]
> -C CA N H
> CA +N C O
> CG CE2 CD2 HD2
> CZ CD2 CE2 HE2
> CD1 CZ CE1 HE1
> CG CE1 CD1 HD1
> CD1 CD2 CG CB
> CE1 CE2 CZ OG
>
> I also modified the aminoacids.hdb and ffbonded.itp accordingly. I then use
> the following command to process the pdb file:
>
> # g_pdb2gmx -f file.pdb -o file.gro -ignh
> ...
> Changing rtp entry of residue 26 SER to 'CSER'
> ...
> Renaming atom 'O' in residue 26 SER to 'OC2'
> ...
>
> The seine before Y2P is changed to CSER, which is the terminal version of
> serine. This creates trouble for further steps to prepare my MD. Is this
> because I have a mistake in defining Y2P entry? Can I force pdb2gmx not
> chaning SER26 to CSER? I can provide additional information if needed.
> Thank you!
>
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
You forgot step 5.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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