[gmx-users] pdb2gmx error

 Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ]  [ atoms ] N N  -0.280 0 H H   0.280 0     CA  

Re: [gmx-users] pdb2gmx error

check your aminoacid.rtp file present in /usr/share/gromacs/top/oplsaa.ff/ check all the atom types of that particular residue in your pdb file and match them properly with the atoms types present in the aminoacid.rtp file .and then proceed On Tue, Jun 12, 2012 at 5:29 PM, delara aghaie

Re: [gmx-users] pdb2gmx error

On 6/12/12 7:59 AM, delara aghaie wrote: Dear Gromacs users Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error: I should mention that I have selected OPLS force field. 1) how can I reach to the conclusion that special forcefield is better fo my syste

[gmx-users] pdb2gmx error

Dear Gromacs users Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error: I should mention that I have selected OPLS force field. 1) how can I reach to the conclusion that special forcefield is better fo my system? 2) This is the error: -

Re: [gmx-users] PDB2GMX error in charmm27 Forcefield

On 2012-04-22 17:11, Mark Abraham wrote: On 22/04/2012 10:58 PM, sai nitin wrote: Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of tha

Re: [gmx-users] PDB2GMX error in charmm27 Forcefield

On 22/04/2012 10:58 PM, sai nitin wrote: Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number

[gmx-users] PDB2GMX error in charmm27 Forcefield

Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this.

Re: [gmx-users] pdb2gmx error

Bishwajit Das wrote: Hi, i attached my pdb file,please check it... fixed.pdb is after fixing it into what if server and actin.pdb is original pdb file.The exact error is The coordinate file is not in an order that Gromacs can work with. It is arranged such that various groups of atoms ar

Re: [gmx-users] pdb2gmx error

Bishwajit Das wrote: when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command in my pdb file then i select AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force field but a error massage came. the massage is following: There are 0 donors a

[gmx-users] pdb2gmx error

when i try to pdb2gmx -f *.pdb -o *_processed.gro -water spce command in my pdb file then i select AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force field but a error massage came. the massage is following: There are 0 donors and 0 acceptors There are 0 h

Re: [gmx-users] pdb2gmx error

Acoot Brett wrote: Hi Mark, The fifth residue of Chain A is Asn, not Val. But Asn also no CG. Standard nomenclature of ASN dictates that there is a CG atom in the side chain. If your input file does not have this atom or it is named incorrectly, it will give rise to the error. -Justi

Re: [gmx-users] pdb2gmx error

Hi Mark,   The fifth residue of Chain A is Asn, not Val. But Asn also no CG.   Acoot From: Acoot Brett To: Discussion list for GROMACS users Sent: Monday, 2 April 2012 10:48 AM Subject: Re: [gmx-users] pdb2gmx error Hi Mark,   I have renumbered the

Re: [gmx-users] pdb2gmx error

: Mark Abraham To: Discussion list for GROMACS users Sent: Monday, 2 April 2012 10:32 AM Subject: Re: [gmx-users] pdb2gmx error On 2/04/2012 10:26 AM, Acoot Brett wrote: Hi Mark, >  >As for the pdb2gmx is the first step, there is still no gro file and rtp file >produced by this s

Re: [gmx-users] pdb2gmx error

y, 2 April 2012 10:22 AM *Subject:* Re: [gmx-users] pdb2gmx error On 2/04/2012 10:19 AM, Acoot Brett wrote: Dear All, I just run a pdb2gmx of a protein, the error message is " Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was

Re: [gmx-users] pdb2gmx error

From: Mark Abraham To: Discussion list for GROMACS users Sent: Monday, 2 April 2012 10:22 AM Subject: Re: [gmx-users] pdb2gmx error On 2/04/2012 10:19 AM, Acoot Brett wrote: Dear All, > >I just run a pdb2gmx of a protein, the error message is " >Fatal err

Re: [gmx-users] pdb2gmx error

Acoot Brett wrote: Dear All, I just run a pdb2gmx of a protein, the error message is " Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 5." According to the sugestion I have tried to find the rea

Re: [gmx-users] pdb2gmx error

On 2/04/2012 10:19 AM, Acoot Brett wrote: Dear All, I just run a pdb2gmx of a protein, the error message is " Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 5." According to the sugestion I have tried

[gmx-users] pdb2gmx error

Dear All,   I just run a pdb2gmx of a protein, the error message is "Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 5."    According to the sugestion I have tried to find the reason in " http://www.grom

[gmx-users] pdb2gmx error message

Dear All,   I meet the following error message for pdb2gmx. Please let me know how to solve this problem.   Cheers,   Wholly  Program pdb2gmx, VERSION 3.3.3 Source code file: futil.c, line: 542 Fatal error: Library file FF.dat not found in current dir nor in default directories. (You can set the d

[gmx-users] pdb2gmx error

Hello everyone I am trying to set up a nucleic acid only simulation using gromacs 4.5.2 pdb2gmx is giving me only options to cap protein terminals and when I choose none it gives the error: "There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry." and exit

Re: [gmx-users] pdb2gmx error

刘文 wrote: hi! I encounter a problen of " Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 426 Fatal error: Residue 'CO' not found in residue topology database" how to solve it? Please search the mailing list archive and the Gromacs wiki when you encounter problems; you wou

[gmx-users] pdb2gmx error

hi! I encounter a problen of " Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 426 Fatal error: Residue 'CO' not found in residue topology database" how to solve it? thank you in advance! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] pdb2gmx error

Thanks, this very helpful!!! Sent from my iPhone On Mar 15, 2009, at 3:48 PM, "Justin A. Lemkul" wrote: Tsjerk Wassenaar wrote: Hi, --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal er

Re: [gmx-users] pdb2gmx error

Tsjerk Wassenaar wrote: Hi, --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1094904186 while adding improper ---

Re: [gmx-users] pdb2gmx error

Hi, >>        --- >>        Program pdb2gmx, VERSION 4.0.3 >>        Source code file: pgutil.c, line: 87 >> >>        Fatal error: >>        Atom N not found in residue 1094904186 while adding improper >> >>        --

Re: [gmx-users] pdb2gmx error

Ilya Chorny wrote: On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul > wrote: Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new re

Re: [gmx-users] pdb2gmx error

On Sat, Mar 14, 2009 at 10:03 PM, Justin A. Lemkul wrote: > > > Ilya Chorny wrote: > >> I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached >> to the side chain nitrogen called ASBG. I want to test the new residue by >> itself. >> >> When I pdb2gmx it I get the following erro

Re: [gmx-users] pdb2gmx error

Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx,

[gmx-users] pdb2gmx error

I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx, VERSION 4.0.3 Source code

Re: [gmx-users] pdb2gmx error

Quoting Gadzikano Munyuki <[EMAIL PROTECTED]>: > I want to do dynamics on a cyclic polypeptide. The peptide contains a residue > that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file > and the aminoacids.dat file.I have put these in the working directory and > also in the lib

Re: [gmx-users] pdb2gmx error

No, but you should try to distinguish an O (letter-O) from a 0 (numeric zero). Tsjerk On Wed, Mar 19, 2008 at 3:54 PM, Gadzikano Munyuki <[EMAIL PROTECTED]> wrote: > I want to do dynamics on a cyclic polypeptide. The peptide contains a residue > that is not standard Ornithine. I have added [ORN]

[gmx-users] pdb2gmx error

I want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file and the aminoacids.dat file.I have put these in the working directory and also in the library. If I grep these files [ORN] is there but i stil

Re: [gmx-users] pdb2gmx error

Gadzikano Munyuki wrote: Hi, i am new to gromacs want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard.I however have included this residue in the ffaoplsaa.rtp file as well as the aminoacids.dat file. When i run pdb2gmx its giving me a fatal error a

[gmx-users] pdb2gmx error

Hi, i am new to gromacs want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard.I however have included this residue in the ffaoplsaa.rtp file as well as the aminoacids.dat file. When i run pdb2gmx its giving me a fatal error and its saying the residue i

[gmx-users] pdb2gmx error

Hi, I have used gromacs simulations before for protein-small molecule. I have not seen this following error previously. All of a sudden, when I run pdb2gmx on my protein file, I get this error below. I did not make any chages to the way my machine is set up or other gromacs related settings, so I

Re: [gmx-users] pdb2gmx error

ikely be unsatisfactory. > > -Justin > > > > > Thanks in advance. > > > > Tawhid > > > > > > > > > > > > - Original Message > > From: Justin A. Lemkul <[EMAIL PROTECTED]> > > To: Discussion list for GROM

Re: [gmx-users] pdb2gmx error

Message > From: Justin A. Lemkul <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Monday, November 26, 2007 9:14:37 PM > Subject: Re: [gmx-users] pdb2gmx error > > Quoting Tawhid Ezaz <[EMAIL PROTECTED]>: > > > Thanks a lot Justin. It worked

Re: [gmx-users] pdb2gmx error

. Lemkul <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, November 26, 2007 9:14:37 PM Subject: Re: [gmx-users] pdb2gmx error Quoting Tawhid Ezaz <[EMAIL PROTECTED]>: > Thanks a lot Justin. It worked really nice. > > now I am stuck with another problem. I nee

Re: [gmx-users] pdb2gmx error

u're trying to do. Please provide more details. -Justin > > Thanks a lot for your help. > > Tawhid > > > > - Original Message > From: Justin A. Lemkul <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Monday, November 26, 2007 7:14

Re: [gmx-users] pdb2gmx error

ent: Monday, November 26, 2007 7:14:43 PM Subject: Re: [gmx-users] pdb2gmx error Quoting Tawhid Ezaz <[EMAIL PROTECTED]>: > Hi, > > I have just started to learn gromacs. I am facing a problem to make topology > file of a myoglobin. I got the pdb file from the csc tutorial. > >

Re: [gmx-users] pdb2gmx error

Quoting Tawhid Ezaz <[EMAIL PROTECTED]>: > Hi, > > I have just started to learn gromacs. I am facing a problem to make topology > file of a myoglobin. I got the pdb file from the csc tutorial. > > When i am running the pdb2gmx with > > pdb2gmx -f conf.pdb -p topol.top > > i get the message, HEME14

[gmx-users] pdb2gmx error

Hi, I have just started to learn gromacs. I am facing a problem to make topology file of a myoglobin. I got the pdb file from the csc tutorial. When i am running the pdb2gmx with pdb2gmx -f conf.pdb -p topol.top i get the message, HEME148 CAB1428 0.569 HEME148 CAC1437 0.562 0.820 N-term

Re: [gmx-users] pdb2gmx error - version 3.3.1

submit a bug report at bugzilla.gromacs.org? On 10/17/2007 2:40 AM, Justin A. Lemkul wrote: Hello all, I am having a strange error when using pdb2gmx. I am trying to generate the topology for a simple protein, using Gromos96 43a1. I am able to create the topology with version 3.3 without issu

[gmx-users] pdb2gmx error - version 3.3.1

Hello all, I am having a strange error when using pdb2gmx. I am trying to generate the topology for a simple protein, using Gromos96 43a1. I am able to create the topology with version 3.3 without issue. However, if I use pdb2gmx under version 3.3.1, I encounter this: $ pdb2gmx -f protein.pdb

Re: [gmx-users] pdb2gmx error

You do not want to use the ffgmx forcefield. For simulating DNA and protein i would use the amber force field. For more info on the ffamber ports see: http://folding.stanford.edu/ffamber/ Tom --On Wednesday, May 30, 2007 04:17:26 -0700 Alaguraj Veluchamy <[EMAIL PROTECTED]> wrote: Dear gmx

Re: [gmx-users] pdb2gmx error

Alaguraj Veluchamy wrote: Dear gmx-users, I am trying to run a simulation of a pdb with DNA molecule. I have give gromacs force fied and the error i found was, There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms chain #res #atoms 1 'A' 162 1245 2 'B' 162 124

[gmx-users] pdb2gmx error

Dear gmx-users, I am trying to run a simulation of a pdb with DNA molecule. I have give gromacs force fied and the error i found was, There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms chain #res #atoms 1 'A' 162 1245 2 'B' 162 1245 3 'C'21417 4 '

Re: [gmx-users] pdb2gmx error

MURAT CETINKAYA wrote: Hi all, I have a small problem with pdb2gmx. I have a non-standard residue with rtp parameters entered manually into oplsaa database. When I try to convert my pdb file into gro, I get: - Program pdb2gmx, VERSION 3.3.1 Source code file: t

[gmx-users] pdb2gmx error

Hi all, I have a small problem with pdb2gmx. I have a non-standard residue with rtp parameters entered manually into oplsaa database. When I try to convert my pdb file into gro, I get: - Program pdb2gmx, VERSION 3.3.1 Source code file: toputil.c, line: 94 Fatal

Re: [gmx-users] pdb2gmx error

Viswanadham Sridhara wrote: Hi Gromacs Users, I am trying to use pdb2gmx with one of the .pdb files, and its says fatal error : in .rtp at line: But it is not displaying any line number in rtp file to look at? any comments or advice to fix this problem or to know the source of the problem?

[gmx-users] pdb2gmx error

Hi Gromacs Users,I am trying to use pdb2gmx with one of the .pdb files, and its says fatal error : in .rtp at line:But it is not displaying any line number in rtp file to look at?any comments or advice to fix this problem or to know the source of the problem? Thanks in advance,-Vishy.-- Viswanadham

Re: [gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

By hand for the topology, check chapter five of the manual. For the gro file use editconf to convert the pdb Hope that helps Tom --On Tuesday, June 13, 2006 17:40:41 +0800 "SUN, Jian" <[EMAIL PROTECTED]> wrote: Dear all, I am doing the simulation of a protein with a small molecular in it

[gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

Dear all,   I am doing the simulation of a protein with a small molecular in its active site. But unfortunately, pdb2gmx cannot generate the gro and top file for the small molecualr? I am using the oplsaa force field, who can tell me how to generate the gro and top files?   Thanks a lot Jian __

[gmx-users] pdb2gmx error

Hello, gmx-users， i used command"pdb2gmx -f a.pdb -ignh" but i got error like: Program pdb2gmx, VERSION 3.3 Source code file: add_par.c, line: 218 Fatal error: Atom H2 not found in rtp database in residue BEN --- there are no H2