Dear All,
I am trying to load a PDB file of CCA-Phe, a ribosomal part, in leap using Antechamber (where C and A are two nucleic acid and Phe is phenyl alanine). When I consider only A-Phe then it successfully loaded as it is neutral system. But when I take CCA-Phe then after addition of hydrogen by ‘reduced’-command in Antechamber the CCA-Phe contain two negative charge in the phosphate diester backbone which is desirable for this system. The problem arises during create the mol2 file from reduced CCA-Phe.pdb file (contain two negative charge) using ‘antechamber’-command. I use the following command (given in Amber tutorial)-
reduced cca1.pdb > cca1_h.pdb
Then I will change the name of residue from ‘C’ and ‘A’ to ‘PHA’ and create a new pdb file : cca1_new.pdb
Then I run the following commands:
antechamber –i cca1_new.pdb –fi pdb –o cca1.mol2 –fo mol2 –c bcc –s 2
Then I noticed the following error-
Running: /usr/local/amber11/bin/bondtype –j full –i ANTECHAMBER_BOND_TYPE.ACO –o ANTECHAMBER_BOND_TYPE.AC –f ac
---Judge bond type for Residue 1 with ID of 74 & Name of PHA---
---Judge bond type for Residue 2 with ID of 75 & Name of PHA---
---Judge bond type for Residue 3 with ID of 76 & Name of PHA---
---Judge bond type for Residue 4 with ID of 77 & Name of PHA---
Running: /usr/local/amber11/bin/atomtype –i ANTECHAMBER_AC.ACO –o ANTECHAMBER_AC.AC –p gaff
Total number of electrons: 532; net charge: 0
Running: /usr/local/amber11/bin/sqm – full –O –i sqm.in –o sqm.out
Error: cannot run “/usr/local/amber11/bin/sqm – full –O –i sqm.in –o sqm.out” of bcc() in charge.c properly, exit
I also attached three pdb file and sqm.out with this mail and wait for hopeful answer.
With the best regards,
Sudarshan
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- application/octet-stream attachment: cca1.pdb
- application/octet-stream attachment: sqm.in
- application/octet-stream attachment: sqm.out
Received on Thu Sep 01 2011 - 06:00:02 PDT
