Alberto Sergio Garay ha scritto:
Dear users
I'm trying to build a polymer with a new building block. I have
included the new
topology block inside the force field rtp file, which I've choosen for
my simulation (ffG53a6.rtp).
I've also prepared a gro input file, where the atoms of each residue
follows the same order as in the rtp file
I also added the new residues names in aminoacids.dat
The problem is: when I run pdb2gmx to obtain the topology of my system
it gives me the following error:
Fatal error:
Atom H1 in residue VBT 2 not found in rtp entry with 24 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation
state.
Option -ignh will ignore all hydrogens in the input.
But there's no H1 atom in my residues. Is pdb2gmx including some extra
atoms to complete my molecule?
Could anyone give any clue about my problem?
Tank you in advance.
Sergio
below there's a part of my rtp file
...
[ VBT ]
[ atoms ]
; name type charge chargegroup
CC1 CH2 0.00000 1
CC2 CH1 0.12000 2
CR1 C -0.12000 3
CR2 C -0.14000 4
HR2 HC 0.14000 4
CR3 C -0.08000 5
HR3 HC 0.08000 5
CR4 C -0.05000 6
CT1 CH2 0.37000 6
NT1 NR -0.32000 6
CR5 C -0.13000 7
HR5 HC 0.13000 7
CR6 C -0.17000 8
HR6 HC 0.17000 8
CT2 C -0.21000 9
HT1 HC 0.21000 9
CT3 C -0.09000 10
CT4 CH3 0.09000 10
CT5 C 0.58000 11
OT1 O -0.58000 11
NT2 NR -0.22000 12
HT2 H 0.22000 12
CT6 C 0.54000 13
OT2 O -0.54000 13
part of my *.gro file
2VBT CC1 21 3.221 5.305 1.589
2VBT CC2 22 3.143 5.334 1.460
2VBT CR1 23 3.115 5.221 1.384
2VBT CR2 24 3.196 5.155 1.293
2VBT HR2 25 3.305 5.159 1.298
2VBT CR3 26 3.132 5.074 1.200
2VBT HR3 27 3.198 5.003 1.151
2VBT CR4 28 2.995 5.068 1.175
2VBT CT1 29 2.948 5.023 1.052
2VBT NT1 30 3.028 5.038 0.928
2VBT CR5 31 2.919 5.144 1.263
2VBT HR5 32 2.810 5.142 1.268
2VBT CR6 33 2.977 5.208 1.372
2VBT HR6 34 2.916 5.232 1.459
2VBT CT2 35 3.070 4.916 0.874
2VBT HT1 36 3.009 4.827 0.860
2VBT CT3 37 3.190 4.911 0.804
2VBT CT4 38 3.245 4.779 0.750
2VBT CT5 39 3.264 5.027 0.784
2VBT OT1 40 3.364 5.030 0.712
2VBT NT2 41 3.224 5.150 0.839
2VBT HT2 42 3.293 5.223 0.844
2VBT CT6 43 3.100 5.156 0.903
2VBT OT2 44 3.076 5.266 0.952
Hi Sergio, you can try this:
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html
and read the FAQ section...
Alessandro
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