[gmx-users] Problem building a new polymer using pdb2gmx....
Alberto Sergio Garay
sgaray at fbcb.unl.edu.ar
Fri Oct 17 13:01:04 CEST 2008
Dear David (van der Spoel)
I made a trial with pdb2gmx using -ter option as you suggested but
without success. I also tried with -inter option but it didn't work.
The program did not give me any chance to reject the option of adding
TER or other kind of atoms. It just gives me the same error. Am I
doing something wrong?
I have also read a lot of messages in the gromacs list related with
pdb2gmx errors but no one give me any idea of how to resolve my
problem. The reading of chapter 5 of gromacs manual neither. I found
in the gromacs list many people complaining about pdb2gmx looked for
atoms which it didn't exist in their pdb's or rtp files. Quite similar
to my problem, but aparently they were able to solve it.
Below I am adding the complete error mesagge of pdb2gmx, may be you
can give any clue of what is happening.
Opening library file ffG53a6.rtp
Opening library file aminoacids.dat
Reading polymer.gro...
Read 'Generated by trjconv : 14 TEQ-VBT 1:1 t= 1750.00024', 309 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 14 residues with 309 atoms
chain #res #atoms
1 '-' 14 309
No occupancies in polymer.gro
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.atp
Atomtype 57
Reading residue database... (ffG53a6)
Opening library file ffG53a6.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 119
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6-c.tdb
Processing chain 1 (309 atoms, 14 residues)
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421
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.
> 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?
>> David van der Spoel wrote:
>> yes. pdb2gmx thinks your molecule is a protein and want to add Hydrogens
>> to the termini. Use the -ter flag and select None.
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
--
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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