[gmx-users] Regarding error.
Dear all gromacs users, While i am running the commond mdrun -deffnm nvt i am getting the following error. Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Kindly tell me how to over come this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, While i am running the commond trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting the following warning. WARNING no output, last frame read at t=10 Kindly tell me how to overcome this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: Regarding error.
-- Forwarded message -- From: Seera Suryanarayana paluso...@gmail.com Date: Fri, Jun 15, 2012 at 1:38 PM Subject: Regarding error. To: gmx-users@gromacs.org Dear all gromacs users, While i am running the commond trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting the following warning. WARNING no output, last frame read at t=10 Kindly tell me how to overcome this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear all gromacs users, I am doing moleculer dynamics by using gromacs software.I got the following error after using the commond mdrun -deffnm nvt. Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated. Kindly tell me how to overcome this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding .mdp files.
Dear all gromacs users, While i am running the commond mdrun -v -deffnm em iam getting the following error. Fatal error: Domain decomposition does not support simple neighbor searching, use gridsearching or use particle decomposition. kindly tell me how to overcome. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear Justin sir, I am simulating a protein 1AKI.pdb which is example of your tutorial.I am doing simulations as your tutorial.I didnt get any errors upto the commond grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr.After this as your tutorial i used the commond mdrun -v -deffnm em, then i got the following error. Fatal error: Domain decomposition does not support simple neighbor searching, use grid searching or use particle decomposition Kindly tell me how to overcome this error. Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, While running the grompp commond after addition of counter ions i am getting the following error. Fatal error: number of coordinates in coordinate file (3ASW_ion.gro, 178301) does not match topology (3ASW.top, 178293) Here i am sending my .top file,kindly tell me how to overcome this error. ; ; File '3ASW.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jun 9 10:36:25 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 3ASW_Protein_chain_A.itp #include 3ASW_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp ;#include ions.itp [ system ] ; Name CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 129 SOL 5 SOL 58209 NA ions 8 /Add NA ions Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, After added the counter ions to the top file and further i used 'grompp' commond,i got the following error. Fatal error: moleculetype CU1 is redefined. This error occurs due the duplication of CU1 in .top file. But i cannot find that error in my .top file.Here i am sending my .top file. Kindly tell me how to overcome this error. ; ; File '1UZ9.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Jun 7 13:55:15 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 1UZ9.pdb -o 1UZ9.gro -p 1UZ9.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 1UZ9_Protein_chain_A.itp #include 1UZ9_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 13532 NA charge 3 /Add NA ions Thanks and regards Suryanarayana Seera, JRF, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: incomplete ring in HIS231 Kindly tell me how to overcome this error and how to correct incomplete ring to complete ring. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, I have 1VZV.pdb file, in that file HIS231 has incomplete ring as N atom is missing.Can i add N atom to the .pdb file if possible how can i add that atom to .pdb file. Suryanarayana Seera, PhD student, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. I wont ignore the 22 missing atoms by using -missing commond. I would like to construct a complete protein structure.But i dont know how to construct the complete protein sturcture.Kindly tell me how to consturct the complete protein and what are the softwares i have to use here. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I've checked [moleculetypes] in topology files and there are not duplicated. I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear Mark, What type of file i have to check for missing of atoms. Thanks and regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, I tried the grompp -c 3I40_ion.gro -p 3I40.top -o 3I40_b4em.tpr -f em.mdp and i got the following error. Option Filename Type Description -f em.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 3I40_ion.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p 3I40.top InputTopology file -pp processed.top Output, Opt. Topology file -o 3I40_b4em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19# Generated 279 of the 1225 non-bonded parameter combinations --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1228 Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Dear all gromacs users, While i am using the commond pdb2gmx -f 4E82.pdb -o 4E82.gro -p 4E82.top.I am getting the following warnings and errors. Warning: Residue EME21 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ILE22 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue SER23 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLY24 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ARG25 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue CYS20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3CYS5 CYS10 CYS20 CYS30 SG18SG36SG75 SG144 SG228 CYS5SG36 0.834 CYS10SG75 0.936 1.000 CYS20 SG144 0.833 0.203 0.935 CYS30 SG228 0.856 0.827 0.200 0.788 CYS31 SG234 0.202 0.860 0.783 0.820 0.734 Linking CYS-3 SG-18 and CYS-31 SG-234... Linking CYS-5 SG-36 and CYS-20 SG-144... Linking CYS-10 SG-75 and CYS-30 SG-228... Start terminus ALA-1: NH3+ End terminus CYS-20: COO- Fatal error: Residue 'EME' not found in residue topology database. Kindly tell me how to over come this error. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, while running the command grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the following error. File input/output error: pr.mdp Please tell me how to over come this error Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding gromacs manual.
Dear all gromacs users, I am new for MD and in particular using gromacs software.I would like to learn basics of gromacs.Please tell me the name of the manual which one is suitable for me. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors.
Dear all gromas users, While i am running the grompp after first mdrun command i got the following error. File input/output error: pr.mdp Is there any explanation why is this happening? I would appreciate any help.I am new in using MD and gromacs in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromas users, While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp after first mdrun command i got the following error. File input/output error: pr.mdp Is there any explanation why is this happening? I would appreciate any help.I am new in using MD and gromacs in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REgarding redefined error.
Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: moleculetype CU1 is redefined Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, HYderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: number of coordinates in coordinate file (1UZ9_ion.gro, 41103) does not match topology (1UZ9.top, 41100) Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors.
Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (208L.top, 62293) Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error.
Dear all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Residue 'CSD' not found in residue topology database Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to over come syntax errors
Dear all Gromacs users, While i am running gromacs software i am getting the following syntax errors. Fatal error: Syntax error - File 1AX8.top, line 7934 Last line read: '## #includeions.itp' I am unable to create _b4em.gro files Is there any explanation why is this happening? I would aooreciate any help.I am new in using MD and gromacs in particular. *Suryanarayana Seera, PhD student, Hyderabad, India.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: How to overcome syntax errors
-- Forwarded message -- From: Seera Suryanarayana paluso...@gmail.com Date: Thu, May 17, 2012 at 12:07 PM Subject: How to overcome syntax errors To: jalem...@vt.edu Dear Justin, While i am running gromacs software i am getting the following syntax errors. Fatal error: Syntax error - File 1AX8.top, line 7934 Last line read: '## #includeions.itp' I am unable to create _b4em.gro files.Please let me know at what position i have to add ## #includeions.itp and Add NA ions or CL ions Is there any explanation why is this happening? I would aooreciate any help.I am new in using MD and gromacs in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding topology error.
DEar all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Topology include file ion.itp not found Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Dear all gromacs users, I tried the grompp and i got the following error.number of coordinates in coordinate file (4INS_b4ion.gro, 90396) does not match topology (4INS.top, 90393). Is there any explanation why is this happens.I would appreceate any help.I am new in using moleculer dynamics and particularly in gromacs. Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. Regards Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding error
Respected Sir, While i am running the gromacs software to simulate the protein i am getting the following error. Fatal error: Residue 'GNP' not found in residue topology database Suryanarayna Seera, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database SURYANARAYANA SEERA, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected Sir, While i am running gromacs software i am getting the following error.Kindly knowing me how to over come the error. Fatal error: number of coordinates in coordinate file (1cys_ion.gro, 99670) does not match topology (1cys.top, 99680) SURYANARAYANA SEERA, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. SURYANARAYANA SEERA, PhD student -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] paluso...@gmail.com
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error
Respected sir, While i am running the gromacs always i am getting the error Residue 'GNP' not found in residue topology database.Kindly tell me the what the error means. Suryanarayana Seera, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
