[gmx-users] adding mdp to amber99sb

[Justin Lemkul]

On 3/1/16 1:14 PM, Irem Altan wrote:
> Hi,
>
> I am trying to add MPD to the amber99sb forcefields. I have added the necessary things to aminoacids.rtp, aminoacids.hdp, and atomtypes.atp, but when I run pdb2gmx I get the following error:
>
> Fatal error:
> Atom type H11 (residue MPD) not found in atomtype database
>
> I’m a bit confused, as I’d have thought H11 would be the atom name and not the atom type because my aminoacids.rtp file contains
>
> [ MPD ]
>   [ atoms ]
>       C    C1          -0.18000    1
>      H1   H11           0.06000    1
>      H1   H12           0.06000    1
>      H1   H13           0.06000    1
>       C    C2           0.26500    1
>       O    O2          -0.68300    1
>       H    H2           0.41800    1
>       C    CM          -0.18000    1
>      HM   HM1           0.06000    1
>      HM   HM2           0.06000    1
>      HM   HM3           0.06000    1
>       C    C3          -0.12000    1
>      H3   H31           0.06000    1
>      H3   H32           0.06000    1
>       C    C4           0.14500    1
>       O    O4          -0.68300    1
>      H4   H41           0.41800    1
>      H4   H42           0.12000    1
>       C    C5          -0.18000    1
>      H5   H51           0.06000    1
>      H5   H52           0.06000    1
>      H5   H53           0.06000    1
>   [ bonds ]
>      C1   H11
>      C1   H12
>      C1   H13
>      C1    C2
>      C2    O2
>      C2    CM
>      O2    H2
>      CM   HM1
>      CM   HM2
>      CM   HM3
>      C2    C3
>      C3   H31
>      C3   H32
>      C3    C4
>      C4    H4
>      C4    O4
>      O4    H4
>      C4    C5
>      C5   H51
>      C5   H52
>      C6   H53
>
> I have added the following to atomtypes.atp:
>
> H1                 1.00800
> H2                 1.00800
> HM                 1.00800
> H3                 1.00800
> H4                 1.00800
> H5                 1.00800
> O2                16.00000
> O4                16.00000
> C1                12.01000
> C2                12.01000
> C3                12.01000
> C4                12.01000
> C5                12.01000
>
> and the aminoacids.hdb:
>
> MPD     14
> 1	2	H4	O4	C4      C3
> 1	2	H2	O2	C2	CM
> 3	4	H5      C5      C4	O4
> 3	4	HM      CM      C2	C3
> 3       4	H1	C1	C2	C3
> 2	6	H3      C3      C4	C2
> 1	5	H4	C4	C5      C3	O4
>
> I have also added the name to the residuetypes.dat file.
>
> What am I overlooking?
>

You inverted name and type in the [atoms] section of the .rtp entry.  It's name, 
type, charge, charge group.  You shouldn't assign the same charge group to every 
atom, but if you're using the Verlet cutoff scheme, it doesn't matter.

-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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