[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

[Justin Lemkul]

On 8/20/15 8:16 AM, Simone Bolognini wrote:
> Thank you for your answer! I did it and now gromacs throws me the following
> error: "Atom HG1 in residue SER 2 was not found in rtp entry SER with 11
> atoms while sorting atoms.". Any clue? Thank you very much.
>

pdb2gmx -ignh

-Justin

> Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul <jalemkul at vt.edu> ha
> scritto:
>
>>
>>
>> On 8/20/15 3:17 AM, Simone Bolognini wrote:
>>> Hi everyone,
>>> I have a .pdb file of the WW domain of human FIP35 protein extracted from
>>> an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3.
>>> Now I need to obtain the topology out of it, but the .pdb contains a
>>> residue, namely HSD, which is not present in the Amber residue database.
>> I
>>> looked at the source files and found out that CHARMM has it. In
>> particular,
>>> this is what you can find in the CHARMM database:
>>>
>>> [ HSD ]
>>>    [ atoms ]
>>> N NH1 -0.47 0
>>> HN H 0.31 1
>>> CA CT1 0.07 2
>>> HA HB 0.09 3
>>> CB CT2 -0.09 4
>>> HB1 HA 0.09 5
>>> HB2 HA 0.09 6
>>> ND1 NR1 -0.36 7
>>> HD1 H 0.32 8
>>> CG CPH1 -0.05 9
>>> CE1 CPH2 0.25 10
>>> HE1 HR1 0.13 11
>>> NE2 NR2 -0.70 12
>>> CD2 CPH1 0.22 13
>>> HD2 HR3 0.10 14
>>> C C 0.51 15
>>> O O -0.51 16
>>>    [ bonds ]
>>> CB CA
>>> CG CB
>>> ND1 CG
>>> CE1 ND1
>>> NE2 CD2
>>> N HN
>>> N CA
>>> C CA
>>> C +N
>>> CA HA
>>> CB HB1
>>> CB HB2
>>> ND1 HD1
>>> CD2 HD2
>>> CE1 HE1
>>> O C
>>> CG CD2
>>> CE1 NE2
>>>    [ impropers ]
>>> ND1 CG CE1 HD1
>>> CD2 CG NE2 HD2
>>> CE1 ND1 NE2 HE1
>>> ND1 CE1 CG HD1
>>> CD2 NE2 CG HD2
>>> CE1 NE2 ND1 HE1
>>> N -C CA HN
>>> C CA +N O
>>>    [ cmap ]
>>> -C N CA C +N
>>>
>>> Is there any possible way in which I can "copy and paste" this in the
>> Amber
>>> database and hope it will work correctly? Thank you very much!!!
>>>
>>
>> No, you can't copy and paste, because then you're mixing force fields and
>> that
>> is bad practice.  HSD is just delta-protonated HIS, which is already in
>> AMBER.
>> It's just called HID, so rename your coordinate files appropriately and
>> you can
>> generate the topology.
>>
>> -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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-- 
==================================================

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

==================================================