[gmx-users] Error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I have tried to sort out this problem with gromacs 2020 and 2019 versions.
I gromacs 2019, It gives:-

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
Atomtype 106
Invalid format:
However, It generates a topology file.
In gromacs 2020, it gives:-

Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

I have modified my atomtypes.atp file as below:-

;[ atomtypes ]
; name  mass
nh 14.01
dnh 14.01
hn 1.008
dhn 1.008
ca 12.01
dca 12.01
nb 14.01
dnb 14.01
h5 1.008
dh5 1.008
nc 14.01
dnc 14.01
cd 12.01
dcd 12.01
na 14.01
dna 14.01
c3 12.01
dc3 12.01
h2 1.008
dh2 1.008
os 16
dos 16
h1 1.008
dh1 1.008
p5 30.97
dp5 30.97
o 16
do 16
oh 16
doh 16
ho 1.008
dho 1.008
h4 1.008
dh4 1.008
c 12.01
dc 12.01
n 14.01
dn 14.01
ha 1.008
dha 1.008
Atomtype 106 is ha, I cant find any thing wrong with it. Could you please
help me to fix this error?

Thanks.
Sadaf
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Re: [gmx-users] error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I have tried to sort out this problem with gromacs 2020 and 2019 versions.
I gromacs 2019, It gives:-

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp
Atomtype 106
Invalid format:
However, It generates a topology file.
In gromacs 2020, it gives:-

Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

I have modified my atomtypes.atp file as below:-

;[ atomtypes ]
; name  mass
nh 14.01
dnh 14.01
hn 1.008
dhn 1.008
ca 12.01
dca 12.01
nb 14.01
dnb 14.01
h5 1.008
dh5 1.008
nc 14.01
dnc 14.01
cd 12.01
dcd 12.01
na 14.01
dna 14.01
c3 12.01
dc3 12.01
h2 1.008
dh2 1.008
os 16
dos 16
h1 1.008
dh1 1.008
p5 30.97
dp5 30.97
o 16
do 16
oh 16
doh 16
ho 1.008
dho 1.008
h4 1.008
dh4 1.008
c 12.01
dc 12.01
n 14.01
dn 14.01
ha 1.008
dha 1.008
Atomtype 106 is ha, I cant find any thing wrong with it. Could you please
help me to fix this error?

Thanks.
Sadaf
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[gmx-users] error in pdb2gmx

[Sadaf Rani]

Dear Gromacs users
I am facing a strange problem while doing pdb2gmx:-
When I use the command:-
 gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It shows the following:-
going to rename ./amber99sb-ildn.ff/aminoacids.r2b
Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b
going to rename ./amber99sb-ildn.ff/dna.r2b
Opening force field file ./amber99sb-ildn.ff/dna.r2b
going to rename ./amber99sb-ildn.ff/rna.r2b
Opening force field file ./amber99sb-ildn.ff/rna.r2b
Reading 74A-G.pdb...
Read '', 4082 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms

  chain  #res #atoms
  1 'A'   489   3970
  2 'B' 3112

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp

---
Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
Invalid atomtype format: ''

However, when I use without gmx, as below:-
pdb2gmx -f 74A-G.pdb -o 74A-G.gro
It generates topology file successfully. What's wrong with the format in
atomtypes.atp I am unable to understand. Could you please help me to find
out?
I have added a new residue to my forcefield file as mentioned in gromacs
manual.
Please correct me where I am wrong, I have added following in
atomtypes.atp file:-
;[ atomtypes ]
; name   bond_type   mass  chargeptype  sigma  eps
  nh 14.01000 0.000   A 3.25000e-1   7.11280e-1
  hn  1.00800 0.000   A 1.06908e-1   6.56888e-2
  ca 12.01000 0.000   A 3.39967e-1   3.59824e-1
  nb 14.01000 0.000   A 3.25000e-1   7.11280e-1
  h5  1.00800 0.000   A 2.42146e-1   6.27600e-2
  nc 14.01000 0.000   A 3.25000e-1   7.11280e-1
  cd 12.01000 0.000   A 3.39967e-1   3.59824e-1
  na 14.01000 0.000   A 3.25000e-1   7.11280e-1
  c3 12.01000 0.000   A 3.39967e-1   4.57730e-1
  h2  1.00800 0.000   A 2.29317e-1   6.56888e-2
  os 16.0 0.000   A 3.1e-1   7.11280e-1
  h1  1.00800 0.000   A 2.47135e-1   6.56888e-2
  p5 30.97000 0.000   A 3.74177e-1   8.36800e-1
   o 16.0 0.000   A 2.95992e-1   8.78640e-1
  oh 16.0 0.000   A 3.06647e-1   8.80314e-1
  ho  1.00800 0.000   A 0.0e+0   0.0e+0
  h4  1.00800 0.000   A 2.51055e-1   6.27600e-2
   c 12.01000 0.000   A 3.39967e-1   3.59824e-1
   n 14.01000 0.000   A 3.25000e-1   7.11280e-1
  ha  1.00800 0.000   A 2.59964e-1   6.27600e-2

Thanks.

Sadaf
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Alright Mark,

pdb2gmx does not give me output file in complete, it crashes before the
generation of top and gro files for the protein, while generating the above
mentioned fatal error.

~Amir

On Mon, Jan 1, 2018 at 11:21 PM, Mark Abraham 
wrote:

> Hi,
>
> Just as Justin said there, I suspect you missed step 5 of
> http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field
>
> pdb2gmx should also have told you things about how many chains, etc. it
> found. What was the full output?
>
> Mark
>
> On Tue, Jan 2, 2018 at 6:52 AM Amir Zeb  wrote:
>
> > Thanks Mark,
> >
> > Actually, the pdb file which I'm trying to execute for topology
> generation,
> > has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
> > directing to command prompt for selection of termini, N-terminus is fine
> > where it is needed for GLN-2, but the app asking C-terminus for THR-14
> > which lies before TYR-15 (in this case TP2-15 which is explained in
> > aforementioned email). I will attach the snap right here to let you clear
> > the query.
> >
> > Select start terminus type for GLN-2
> >  0: NH3+
> >  1: NH2
> >  2: 5TER
> >  3: None
> > 0
> > Start terminus GLN-2: NH3+
> > Select end terminus type for THR-14
> >  0: COO-
> >  1: COOH
> >  2: CT2
> >  3: 3TER
> >  4: None
> > 0
> > End terminus THR-14: COO-
> > Opening force field file ./charmm36-jul2017.ff/merged.arn
> >
> > So, I don't why am I getting this comment? The C-terminal residue of my
> pdb
> > file is SER-287. Please let me know if possible why C-terminus is needed
> > for THR-14 of the pdb file? If you kindly need more information, I will
> go
> > through.
> >
> > Also, some has faced the similar issue here:
> >
> >
> > https://www.researchgate.net/post/How_can_I_prevent_
> GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_
> phosphorylated_amino_acid_as_a_C-terminal
> >
> >
> > But I couldn't follow, how to resolve it?
> >
> > Thanks!
> >
> > ~Amir
> >
> > On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > I would rename those atoms exactly as the .tdb file in your force field
> > > expects. And if that doesn't work, try deleting them and having pdb2gmx
> > > rebuild them.
> > >
> > > Mark
> > >
> > > On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb  wrote:
> > >
> > > > Hi gmx users,
> > > >
> > > > Wishing you all a very happy new year 2k18.
> > > >
> > > > I have modified a particular Tyr residue to phosphorylated Tyr and
> > > renamed
> > > > as TP2 per forcefield recognizable name. I have used:
> > > > gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> > > > C36m ff
> > > > Gromacs v5.0.6
> > > > NH3+ as N-terminus
> > > > COO- as C-terminus
> > > > TIP3P water model
> > > >
> > > > I am getting error:
> > > >
> > > > Fatal error:
> > > > Atom OXT in residue SER 287 was not found in rtp entry SER with 11
> > atoms
> > > > while sorting atoms.
> > > >
> > > > The C-terminus of my pdb file is pasted right here:
> > > > ATOM   4538  OC1 SER A 287
> > > > ATOM   4539  OC2 SER A 287
> > > > TER  4540   SER A 287
> > > > END
> > > >
> > > > I am aware of that SER 287 is C-terminus residue but by which name
> > > should i
> > > > replace the terminal oxygen to cope with this error?
> > > >
> > > > Looking forward for your kind suggestions.
> > > >
> > > > Thanks in advance!
> > > >
> > > > ~Amir
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
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> > > Support/Mailing_Lists/GMX-Users_List before posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Mark Abraham]

Hi,

Just as Justin said there, I suspect you missed step 5 of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

pdb2gmx should also have told you things about how many chains, etc. it
found. What was the full output?

Mark

On Tue, Jan 2, 2018 at 6:52 AM Amir Zeb  wrote:

> Thanks Mark,
>
> Actually, the pdb file which I'm trying to execute for topology generation,
> has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
> directing to command prompt for selection of termini, N-terminus is fine
> where it is needed for GLN-2, but the app asking C-terminus for THR-14
> which lies before TYR-15 (in this case TP2-15 which is explained in
> aforementioned email). I will attach the snap right here to let you clear
> the query.
>
> Select start terminus type for GLN-2
>  0: NH3+
>  1: NH2
>  2: 5TER
>  3: None
> 0
> Start terminus GLN-2: NH3+
> Select end terminus type for THR-14
>  0: COO-
>  1: COOH
>  2: CT2
>  3: 3TER
>  4: None
> 0
> End terminus THR-14: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
>
> So, I don't why am I getting this comment? The C-terminal residue of my pdb
> file is SER-287. Please let me know if possible why C-terminus is needed
> for THR-14 of the pdb file? If you kindly need more information, I will go
> through.
>
> Also, some has faced the similar issue here:
>
>
> https://www.researchgate.net/post/How_can_I_prevent_GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_phosphorylated_amino_acid_as_a_C-terminal
>
>
> But I couldn't follow, how to resolve it?
>
> Thanks!
>
> ~Amir
>
> On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > I would rename those atoms exactly as the .tdb file in your force field
> > expects. And if that doesn't work, try deleting them and having pdb2gmx
> > rebuild them.
> >
> > Mark
> >
> > On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb  wrote:
> >
> > > Hi gmx users,
> > >
> > > Wishing you all a very happy new year 2k18.
> > >
> > > I have modified a particular Tyr residue to phosphorylated Tyr and
> > renamed
> > > as TP2 per forcefield recognizable name. I have used:
> > > gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> > > C36m ff
> > > Gromacs v5.0.6
> > > NH3+ as N-terminus
> > > COO- as C-terminus
> > > TIP3P water model
> > >
> > > I am getting error:
> > >
> > > Fatal error:
> > > Atom OXT in residue SER 287 was not found in rtp entry SER with 11
> atoms
> > > while sorting atoms.
> > >
> > > The C-terminus of my pdb file is pasted right here:
> > > ATOM   4538  OC1 SER A 287
> > > ATOM   4539  OC2 SER A 287
> > > TER  4540   SER A 287
> > > END
> > >
> > > I am aware of that SER 287 is C-terminus residue but by which name
> > should i
> > > replace the terminal oxygen to cope with this error?
> > >
> > > Looking forward for your kind suggestions.
> > >
> > > Thanks in advance!
> > >
> > > ~Amir
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> >
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Thanks Mark,

Actually, the pdb file which I'm trying to execute for topology generation,
has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
directing to command prompt for selection of termini, N-terminus is fine
where it is needed for GLN-2, but the app asking C-terminus for THR-14
which lies before TYR-15 (in this case TP2-15 which is explained in
aforementioned email). I will attach the snap right here to let you clear
the query.

Select start terminus type for GLN-2
 0: NH3+
 1: NH2
 2: 5TER
 3: None
0
Start terminus GLN-2: NH3+
Select end terminus type for THR-14
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
0
End terminus THR-14: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn

So, I don't why am I getting this comment? The C-terminal residue of my pdb
file is SER-287. Please let me know if possible why C-terminus is needed
for THR-14 of the pdb file? If you kindly need more information, I will go
through.

Also, some has faced the similar issue here:

https://www.researchgate.net/post/How_can_I_prevent_GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_phosphorylated_amino_acid_as_a_C-terminal


But I couldn't follow, how to resolve it?

Thanks!

~Amir

On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham 
wrote:

> Hi,
>
> I would rename those atoms exactly as the .tdb file in your force field
> expects. And if that doesn't work, try deleting them and having pdb2gmx
> rebuild them.
>
> Mark
>
> On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb  wrote:
>
> > Hi gmx users,
> >
> > Wishing you all a very happy new year 2k18.
> >
> > I have modified a particular Tyr residue to phosphorylated Tyr and
> renamed
> > as TP2 per forcefield recognizable name. I have used:
> > gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> > C36m ff
> > Gromacs v5.0.6
> > NH3+ as N-terminus
> > COO- as C-terminus
> > TIP3P water model
> >
> > I am getting error:
> >
> > Fatal error:
> > Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
> > while sorting atoms.
> >
> > The C-terminus of my pdb file is pasted right here:
> > ATOM   4538  OC1 SER A 287
> > ATOM   4539  OC2 SER A 287
> > TER  4540   SER A 287
> > END
> >
> > I am aware of that SER 287 is C-terminus residue but by which name
> should i
> > replace the terminal oxygen to cope with this error?
> >
> > Looking forward for your kind suggestions.
> >
> > Thanks in advance!
> >
> > ~Amir
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Error regarding pdb2gmx of modified residue

[Mark Abraham]

Hi,

I would rename those atoms exactly as the .tdb file in your force field
expects. And if that doesn't work, try deleting them and having pdb2gmx
rebuild them.

Mark

On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb  wrote:

> Hi gmx users,
>
> Wishing you all a very happy new year 2k18.
>
> I have modified a particular Tyr residue to phosphorylated Tyr and renamed
> as TP2 per forcefield recognizable name. I have used:
> gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> C36m ff
> Gromacs v5.0.6
> NH3+ as N-terminus
> COO- as C-terminus
> TIP3P water model
>
> I am getting error:
>
> Fatal error:
> Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
> while sorting atoms.
>
> The C-terminus of my pdb file is pasted right here:
> ATOM   4538  OC1 SER A 287
> ATOM   4539  OC2 SER A 287
> TER  4540   SER A 287
> END
>
> I am aware of that SER 287 is C-terminus residue but by which name should i
> replace the terminal oxygen to cope with this error?
>
> Looking forward for your kind suggestions.
>
> Thanks in advance!
>
> ~Amir
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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[gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Hi gmx users,

Wishing you all a very happy new year 2k18.

I have modified a particular Tyr residue to phosphorylated Tyr and renamed
as TP2 per forcefield recognizable name. I have used:
gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
C36m ff
Gromacs v5.0.6
NH3+ as N-terminus
COO- as C-terminus
TIP3P water model

I am getting error:

Fatal error:
Atom OXT in residue SER 287 was not found in rtp entry SER with 11 atoms
while sorting atoms.

The C-terminus of my pdb file is pasted right here:
ATOM   4538  OC1 SER A 287
ATOM   4539  OC2 SER A 287
TER  4540   SER A 287
END

I am aware of that SER 287 is C-terminus residue but by which name should i
replace the terminal oxygen to cope with this error?

Looking forward for your kind suggestions.

Thanks in advance!

~Amir
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Re: [gmx-users] Error in pdb2gmx

[Mark Abraham]

Hi,

Google knows that better than I ;-)

Mark

On Mon, 31 Jul 2017 17:11 Souvik Dey  wrote:

> Can you name some of these softwares? I am relatively new in this.
>
> On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You need to build in the residue in a way that makes sense. Using some
> > other software, but there are some suggestions on the Gromacs website.
> >
> > Mark
> >
> > On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:
> >
> > > Hi,
> > >
> > > I am trying to run pdb2gmx on a long Amino Acid chain. However, one of
> > the
> > > residues in the middle is incomplete. If I change the residue manually
> > > myself, would there be any problem in connectivity? Else, how do I sort
> > out
> > > this problem?
> > >
> > > Souvik
> > >
> > > --
> > > Souvik Dey
> > > Integrated Science Education & Research Centre
> > > Visva Bharati University
> > > Santiniketan-731235
> > > West Bengal
> > > 8981736643
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
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Re: [gmx-users] Error in pdb2gmx

[Souvik Dey]

Can you name some of these softwares? I am relatively new in this.

On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham 
wrote:

> Hi,
>
> You need to build in the residue in a way that makes sense. Using some
> other software, but there are some suggestions on the Gromacs website.
>
> Mark
>
> On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:
>
> > Hi,
> >
> > I am trying to run pdb2gmx on a long Amino Acid chain. However, one of
> the
> > residues in the middle is incomplete. If I change the residue manually
> > myself, would there be any problem in connectivity? Else, how do I sort
> out
> > this problem?
> >
> > Souvik
> >
> > --
> > Souvik Dey
> > Integrated Science Education & Research Centre
> > Visva Bharati University
> > Santiniketan-731235
> > West Bengal
> > 8981736643
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] Error in pdb2gmx

[Mark Abraham]

Hi,

You need to build in the residue in a way that makes sense. Using some
other software, but there are some suggestions on the Gromacs website.

Mark

On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:

> Hi,
>
> I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the
> residues in the middle is incomplete. If I change the residue manually
> myself, would there be any problem in connectivity? Else, how do I sort out
> this problem?
>
> Souvik
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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[gmx-users] Error in pdb2gmx

[Souvik Dey]

Hi,

I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the
residues in the middle is incomplete. If I change the residue manually
myself, would there be any problem in connectivity? Else, how do I sort out
this problem?

Souvik

-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] Error in pdb2gmx command (Justin Lemukel)

[Justin Lemkul]

On 4/17/17 3:24 AM, Yogendra Patel wrote:

Hello gromacs users,

I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs
4.5.5. While running the pdb2gmx to generate the topology, I'm getting the
error as follows. I have kept the modified rtp file, pdb file and modified
ffbonded.itp file in my working folder. The rtp file has been named as


Then that's your problem.  Files in the working directory are not being read, 
instead you are reading everything out of $GMXLIB/charmm27.ff, as the pdb2gmx 
output notes.  If you want to modify force field files locally, you must create 
an entire force field directory, modify the files within it, then choose that 
directory when prompted by pdb2gmx.


-Justin


aminoacids.rtp same as mentioned in gromacs top folder .Please suggest and
help.


Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading i-paa@30_2.pdb...
Read 257 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 30 residues with 257 atoms

  chain  #res #atoms
  1 ' '30257

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 43
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 47
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 59
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 63
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.10#
Processing chain 1 (257 atoms, 30 residues)
Identified residue PAHb1 as a starting terminus.
Identified residue PAHe30 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581

Fatal error:
Residue 'PAHb' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Error in pdb2gmx command (Justin Lemukel)

[Yogendra Patel]

Hello gromacs users,

I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs
4.5.5. While running the pdb2gmx to generate the topology, I'm getting the
error as follows. I have kept the modified rtp file, pdb file and modified
ffbonded.itp file in my working folder. The rtp file has been named as
aminoacids.rtp same as mentioned in gromacs top folder .Please suggest and
help.


Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading i-paa@30_2.pdb...
Read 257 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 30 residues with 257 atoms

  chain  #res #atoms
  1 ' '30257

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 43
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 47
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 59
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 63
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.10#
Processing chain 1 (257 atoms, 30 residues)
Identified residue PAHb1 as a starting terminus.
Identified residue PAHe30 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581

Fatal error:
Residue 'PAHb' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
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Re: [gmx-users] error in pdb2gmx

[Justin Lemkul]

On 4/17/16 12:05 AM, Shahla Omidi wrote:

​hello
I want to simulate my protein with charmm36, and I used gromacs505 for this
I took this error with pdb2gmx
"Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed."
residue 1 is not "proline" in my protein and I dont know what I should do to 
solve this problem
could you help me?



Please provide your full command and the entire screen output so we can see the 
selections and how pdb2gmx is parsing the chains.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] error in pdb2gmx

[Shahla Omidi]

​hello
I want to simulate my protein with charmm36, and I used gromacs505 for this
I took this error with pdb2gmx
"Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed."
residue 1 is not "proline" in my protein and I dont know what I should do to 
solve this problem
could you help me?

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Re: [gmx-users] error using pdb2gmx

[Irem Altan]

Alright, thank you! Apologies to everyone for duplicate e-mails.

Best,
Irem

> On Jan 6, 2016, at 4:23 PM, Mark Abraham  wrote:
> 
> Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-)
> 
> Mark
> 
> On Wed, Jan 6, 2016 at 9:35 PM Irem Altan  wrote:
> 
>> Hi,
>> 
>> I have a .pdb file that I generated by creating three more copies of the
>> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
>> on it, but I get the following error:
>> 
>> Fatal error:
>> Residue 111 named CYS of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom CA used in
>> that entry is not found in the input file. Perhaps your atom
>> and/or residue naming needs to be fixed.
>> 
>> What is weird is that there is no residue 111 that is a cysteine (residue
>> 111 is a phenylalanine). I had run MD simulations successfully on a single
>> copy of this protein before. pdb2gmx runs without an error when I use the
>> old .pdb file. What could be the problem?
>> 
>> Best,
>> Irem
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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[gmx-users] error using pdb2gmx

[Irem Altan]

Hi,

I have a .pdb file that I generated by creating three more copies of the 
protein according to its P212121 symmetry. I am now trying to run pdb2gmx on 
it, but I get the following error:

Fatal error:
Residue 111 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

What is weird is that there is no residue 111 that is a cysteine (residue 111 
is a phenylalanine). I had run MD simulations successfully on a single copy of 
this protein before. pdb2gmx runs without an error when I use the old .pdb 
file. What could be the problem?

Best,
Irem
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[gmx-users] error using pdb2gmx

[Irem Altan]

Hi,

I have a .pdb file that I generated by creating three more copies of the 
protein according to its P212121 symmetry. I am now trying to run pdb2gmx on 
it, but I get the following error:

Fatal error:
Residue 111 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

What is weird is that there is no residue 111 that is a cysteine (residue 111 
is a phenylalanine). I had run MD simulations successfully on a single copy of 
this protein before. pdb2gmx runs without an error when I use the old .pdb 
file. What could be the problem?

Best,
Irem
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Re: [gmx-users] error using pdb2gmx

[Mark Abraham]

Hi,

You don't need to run pdb2gmx to generate copies, just edit the [system]
field of your topology to match your coordinate file.

Mark

On Wed, Jan 6, 2016 at 8:38 PM Irem Altan  wrote:

> Hi,
>
> I have a .pdb file that I generated by creating three more copies of the
> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
> on it, but I get the following error:
>
> Fatal error:
> Residue 111 named CYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> What is weird is that there is no residue 111 that is a cysteine (residue
> 111 is a phenylalanine). I had run MD simulations successfully on a single
> copy of this protein before. pdb2gmx runs without an error when I use the
> old .pdb file. What could be the problem?
>
> Best,
> Irem
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> * Please search the archive at
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> posting!
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Re: [gmx-users] error using pdb2gmx

[Mark Abraham]

Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-)

Mark

On Wed, Jan 6, 2016 at 9:35 PM Irem Altan  wrote:

> Hi,
>
> I have a .pdb file that I generated by creating three more copies of the
> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
> on it, but I get the following error:
>
> Fatal error:
> Residue 111 named CYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> What is weird is that there is no residue 111 that is a cysteine (residue
> 111 is a phenylalanine). I had run MD simulations successfully on a single
> copy of this protein before. pdb2gmx runs without an error when I use the
> old .pdb file. What could be the problem?
>
> Best,
> Irem
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] Error using pdb2gmx tool

[ankit agrawal]

hi,
I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
water molecule from molecule then ran the following command.

pdb2gmx -f 4APX.pdb -water tip3p

then I chose force field : CHARMM27 (with CMAP) after that it should create
3 types of files  (.gro, .itp, .top) but it is not generating the .gro file
and showing an error.
Fatal error: Residue 'CA' not found in residue topology database.

Please help me to solve this error.
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Re: [gmx-users] Error using pdb2gmx tool

[Justin Lemkul]

On 8/21/14, 5:24 AM, ankit agrawal wrote:

hi,
I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
water molecule from molecule then ran the following command.

pdb2gmx -f 4APX.pdb -water tip3p

then I chose force field : CHARMM27 (with CMAP) after that it should create
3 types of files  (.gro, .itp, .top) but it is not generating the .gro file
and showing an error.
Fatal error: Residue 'CA' not found in residue topology database.



Calcium ions are called CAL in CHARMM.  Rename the residue(s) in the .pdb 
file.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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