[gmx-users] Problem building a new polymer using pdb2gmx....
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 17 13:27:43 CEST 2008
Alberto Sergio Garay wrote:
> 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.
please give the whole command line
pdb2gmx -ignh -ter should be OK, but if you nee dhydrogens you also have
to make/update the hdb file.
>
> 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
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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