[gmx-users] pdb2gmx assign CSER to non-terminal serine
Zheng Ruan
zruan1991 at gmail.com
Tue May 3 18:09:02 CEST 2016
Thank you Justin!!! That's the problem. Now everything runs well.
Ruan
On Tue, May 3, 2016 at 12:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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